Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	1,608,040	Δ1 bp	85.7%	intergenic (+310/‑37)	RCAP_rcc01484 → / → murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase

Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_014034	1,608,040	0	G→.	85.7%	8.7 ‑1.7 ‑0.5	28	intergenic (+310/‑37)	RCAP_rcc01484/murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase
Reads supporting (aligned to +/- strand):  new base (4/20):  ref base (2/2):  total (6/22)
Fisher's exact test strand distribution p-value = 1.91e-01
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 3.04e-01

TCTTCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCCTTGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGGCCGCGCGGCGCGGGCCCAATTCACCCCCGCAGCTTACGGA  >  NC_014034/1607940‑1608068                                                                                                      |                             gtctCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAAGGGGGGCTGCGCGCCCCCCCCTT.GCCCCcccggcgcgg                             >  1:837581/4‑101 (MQ=255)  tctCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCgc.tggcgcggcc                           <  1:779051/99‑3 (MQ=38)   ctCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGCGGCcc                          <  2:2466092/100‑1 (MQ=38)   ctCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGCGGCcc                          >  1:4203524/2‑101 (MQ=38)   ctCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGCGGCcc                          >  1:368559/2‑101 (MQ=38)    tCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGCGGCcca                         <  2:558129/101‑2 (MQ=38)      cGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAAt                      <  1:2243143/101‑1 (MQ=37)      cGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCCTGGTCCGC.TGGCGC.GGCCCAAt                      >  2:1782260/1‑101 (MQ=255)       gACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAAtt                     <  1:1061500/101‑1 (MQ=37)       gACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAAtt                     <  2:11731/101‑1 (MQ=37)         ccTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCa                   <  1:828935/101‑1 (MQ=37)            tttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAccc                <  2:2724014/101‑1 (MQ=38)            tttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAccc                <  1:3708017/101‑1 (MQ=37)             ttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAcccc               >  2:3088370/1‑101 (MQ=38)             ttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAcccc               <  1:959689/101‑1 (MQ=38)             ttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAcccc               <  1:677789/101‑1 (MQ=37)              tCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAccccc              <  1:3004073/101‑1 (MQ=38)               cccAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCg             <  2:159319/101‑1 (MQ=38)                ccAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGc            <  1:1880069/101‑1 (MQ=38)                 cAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcg           >  1:1497020/1‑100 (MQ=38)                  aGCGGATCCCGCGACGGGGTGCGACGCC.TGCAGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgg          <  1:4066694/101‑3 (MQ=37)                    cGGATCCCGCGACGGGGTGCGGCGCC.TGCGGCCCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcggga        <  1:2791024/101‑5 (MQ=25)                    cGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcggga        >  2:1869800/1‑97 (MQ=37)                    cGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATCCACCCCCGcggga        >  2:1133022/1‑97 (MQ=37)                     agATCTCGAGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGC.CCGGCCCAATCCACCCCCGcgggat       <  2:3422457/100‑6 (MQ=19)                       gtCCCGCGGCGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggatat     <  1:4066160/100‑8 (MQ=25)                       aTCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggatat     <  1:10768/101‑8 (MQ=37)                        tCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggatatt    <  1:1048526/101‑9 (MQ=37)                        tCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggatatt    <  1:4175435/101‑9 (MQ=37)                          ccGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggatatttc  <  2:3109789/101‑11 (MQ=25)                          ccGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggatatttc  <  2:439932/101‑11 (MQ=25)                          ccGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggatatttc  <  1:2662624/101‑11 (MQ=25)                                                                                                      |                             TCTTCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCCTTGCGGCGCCGCCCG.AAAGGGGGGCTGCGCGCCCCCCTCTTGGGCCGCGCGGCGCGGGCCCAATTCACCCCCGCAGCTTACGGA  >  NC_014034/1607940‑1608068 Base quality scores:  ATCG  < 3 ≤  ATCG  < 19 ≤  ATCG  < 25 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG