Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,657,785	G→C	13.9%	intergenic (‑91/‑161)	tktA ← / → sahR	transketolase A/methionine metabolism transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,657,785	0	G	C	13.9%	89.6 / 8.1	36	intergenic (‑91/‑161)	tktA/sahR	transketolase A/methionine metabolism transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (16/14);  new base C (3/2);  total (19/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.16e-01

GGCATCCATGCTGAGGGCACGAATGGCGTTGGCACGTTCACGACGGCTGGGCATCGCTGATCTCCTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACTTTTTGATATTGGCCTTGCTAGGGCATCGATGCCTGTC  >  NC_002947/5657641‑5657931                                                                                                                                                   |                                                                                                                                                   ggCATCCATGCTGAGGGCACGAATGGCGTTGGCACGTTCACGACGGCTGGGCATCGCTGATCTCCTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGCCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTaagcgcc                                                                                                                                                  >  4:113277/1‑147 (MQ=255)     tCCATGCTGAGGGCACGAATGGCGTTGGCACGTTCACGACGGCTGGGCATCGCTGATCTCCTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTaagcgccaagcgc                                                                                                                                            <  7:43345/149‑1 (MQ=255)           cTGAGGGAACTATTGGGGTTGGAAGTTTCACGACGGCTGGCCTTCGCTTATCTCTTAGGGGGCTTGAATAGGTGCTACTTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCgg                                                                                                                                         <  1:100177/148‑1 (MQ=255)               gggCACGAATGGCGTTGGCACGTTCACGACGGCTGGGCATCGCTGATCTCCTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAg                                                                                                                                  >  7:42452/1‑149 (MQ=255)                      aaTGGCGTTGGCACGTTCACGACGGCTGGGCATCGCTGATCTCCTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAAc                                                                                                                           <  8:42452/149‑1 (MQ=255)                          gCGTTGGCACGTTCACGACGGCTGGGCATCGCTGATCTCCTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTgaa                                                                                                                       >  3:43907/1‑149 (MQ=255)                               ggCACGTTCACGACGGCTGGGCATCGCTGATCTCCTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGaagaag                                                                                                                   <  2:88046/148‑1 (MQ=255)                                          gacgGCTGGGCATCGCTGATCTCCTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGc                                                                                                                                        <  8:155866/116‑1 (MQ=255)                                              gCTGGGCATCGCTGATCTCCTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCggg                                                                                                   <  4:43907/149‑1 (MQ=255)                                                    cATCGCTGATCTCCTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAgcgc                                                                                                           >  6:231111/1‑135 (MQ=255)                                                    cATCGCTGATCTCCTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAgcgc                                                                                                           <  5:231111/135‑1 (MQ=255)                                                                ccTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCag                                                                                                                >  2:29299/1‑118 (MQ=255)                                                                ccTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTaa                                                                                 >  1:140126/1‑149 (MQ=255)                                                                 cTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAAc                                                                                >  3:170448/1‑149 (MQ=255)                                                                      gggCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAg                                                                           <  4:170448/149‑1 (MQ=255)                                                                                      t‑‑gtCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGc                                                           >  2:182500/1‑149 (MQ=255)                                                                                         gtCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGc                                                           >  4:301795/1‑148 (MQ=255)                                                                                             cGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATc                                                      >  4:221345/1‑149 (MQ=255)                                                                                              gAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCgt                                                                                     >  4:273506/1‑117 (MQ=255)                                                                                               aaaaaGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGc                                                    >  3:273469/1‑149 (MQ=255)                                                                                                       ggcCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCa                                            <  4:273469/149‑1 (MQ=255)                                                                                                                cGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACtttt                                    <  3:113277/148‑1 (MQ=255)                                                                                                                cGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACtttt                                    <  5:138442/148‑1 (MQ=255)                                                                                                                 gCCCACTGGGGGCGCTTGGGTCAAACATTTAAGCTCCAAGAGCCGGATTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGTTGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACttttt                                   <  5:268472/148‑1 (MQ=255)                                                                                                                  cccACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACTTTTTGa                                 >  7:195683/1‑149 (MQ=255)                                                                                                                         ggggCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAAAGTTTTGATATTgg                           <  3:301795/148‑1 (MQ=255)                                                                                                                          cggcgcttggcgcttAAATGTTTGCCCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCaaa                                                                                         <  5:53996/84‑1 (MQ=21)                                                                                                                          cggcgcttggcgcttAAATGTTTGCCCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCaaa                                                                                         >  6:53996/2‑85 (MQ=21)                                                                                                                          cggcgcttggcgcttAAATGTTTGCCCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACTTTTTGATATTGGcc                         >  5:128425/2‑149 (MQ=38)                                                                                                                           ggcgcttggcgcttAAATGTTTGCCCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCa                                            <  2:233678/129‑1 (MQ=38)                                                                                                                           ggcgcttggcgcttAAATGTTTGCCCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCa                                            >  1:233678/1‑129 (MQ=38)                                                                                                                           ggCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGCGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACTTTTTGATATTGGCCt                        >  8:50478/1‑149 (MQ=255)                                                                                                                                   gggCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACTTTTTGATATTGGCCTTGCTAggg                >  1:219523/1‑149 (MQ=255)                                                                                                                                    ggCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACTTTTTGATATTGGCCTTGCTAggg                >  3:237323/1‑148 (MQ=255)                                                                                                                                       aaaCATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACTTTTTGATATTGGCCTTGCTAGGGCATc            >  3:311244/1‑149 (MQ=255)                                                                                                                                          cATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACTTTTTGATATTGGCCTTGCTAGGGCATCGAt         <  2:140126/149‑1 (MQ=255)                                                                                                                                            tttAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACTTTTTGATATTGGCCTTGCTAGGGCATCGATGc       <  3:221345/149‑1 (MQ=255)                                                                                                                                            tttAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACTTTTTGATATTGGCCTTGCTAGGGCATCGATGc       <  7:50478/149‑1 (MQ=255)                                                                                                                                                   gccaagcgccGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACTTTTTGATATTGGCCTTGCTAGGGCATCGATGCCTGTc  >  6:7326/1‑147 (MQ=255)                                                                                                                                                   gccaagcgccGGCTTTAAGCCGCAACTGAAGAACCAGAGCGCGACTCGGGGCGCCCCAAAGCCTGTAACTTGAGGCTTTCGCCTTGCAGCTCATCGCCAATATCAAAACTTTTTCATATTGGCCTTGCTAGCGCATCGAAGCCTGTc  >  6:106439/1‑147 (MQ=255)                                                                                                                                                   |                                                                                                                                                   GGCATCCATGCTGAGGGCACGAATGGCGTTGGCACGTTCACGACGGCTGGGCATCGCTGATCTCCTAGGGGGCTTGAATAGGTGGT‑‑GTCACGAAAAAGGCGGCCATTTTCGCCCACTGGGGGCGCTTGGGGCAAACATTTAAGCGCCAAGCGCCGGCTTTAAGCCGCAACTGAAGAAGCAGAGCGCGACTCGGGGCGCCCCAAAGCGTGTAACTTGAGGCTTTCGGCTTGCAGCTCATCGCCAATATCAAAACTTTTTGATATTGGCCTTGCTAGGGCATCGATGCCTGTC  >  NC_002947/5657641‑5657931

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑