Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	1,608,040	Δ1 bp	75.0%	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→.	75.0%	14.4 ‑0.6 ‑0.5	20	intergenic (+310/‑37)	RCAP_rcc01484/murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase
Reads supporting (aligned to +/- strand):  new base (3/12):  ref base (0/5):  total (3/17)
Fisher's exact test strand distribution p-value = 5.39e-01
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 3.01e-01

TTCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCCTTGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGGCCGCGCGGCGCGGGCCCAATTCACCCCCGCAGCTTACGG  >  NC_014034/1607942‑1608067                                                                                                   |                            ctCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGCGGCcc                         <  2:81148/100‑1 (MQ=38) ctCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGCGGCcc                         <  2:2807904/100‑1 (MQ=38)  tCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCGGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGCGGCcca                        <  2:2947778/101‑2 (MQ=37)  tCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGCGGCcca                        <  2:1780719/101‑2 (MQ=38)  tCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGCGGCcca                        <  1:2801641/101‑2 (MQ=38)    cGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAAt                     <  2:3011706/101‑1 (MQ=38)     gACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAAtt                    <  1:1155841/101‑1 (MQ=38)     gACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAAtt                    <  2:1796780/101‑1 (MQ=37)     gACCTTATCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAAtt                    <  1:748767/101‑1 (MQ=37)          tttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAccc               >  1:3453610/1‑101 (MQ=38)          tttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCCCTTGGTCCGC.TGGCGC.GGCCCCATTCAccc               >  1:4197305/1‑101 (MQ=255)           ttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAcccc              <  1:3106053/101‑1 (MQ=37)            tCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAccccc             <  1:1386705/101‑1 (MQ=37)             cccAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCg            <  2:4643939/101‑1 (MQ=38)              ccAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGc           <  2:3448334/101‑1 (MQ=38)                aGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgg         <  2:2703484/101‑3 (MQ=37)                 gCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcggg        <  1:548442/101‑4 (MQ=37)                  cGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcggga       >  2:209874/1‑97 (MQ=37)                    gATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggata     <  2:1798646/101‑7 (MQ=37)                      tCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGCG.GGCGC.GGCCCAATTCATCCCCGcgggggatt   >  1:854201/1‑93 (MQ=25)                       cccGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggatattt  <  1:120329/101‑10 (MQ=25)                                                                                                   |                            TTCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCCTTGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGGCCGCGCGGCGCGGGCCCAATTCACCCCCGCAGCTTACGG  >  NC_014034/1607942‑1608067 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 22 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG