Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	357,591	C→T	intergenic (+137/+200)	codA → / ← cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,591	0	C	T	100.0%	95.2 / NA	40	intergenic (+137/+200)	codA/cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (20/20);  total (20/20)

ACTGGGTTACAGCGAGCTTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTCCTCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCA  >  NC_000913/357458‑357725                                                                                                                                      |                                                                                                                                       aCTGGGTTACAGCGAGCTTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCg                                                                                                                                   <  1:675623/139‑1 (MQ=255)   tGGGTTACAGCGAGCTTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTg                                                                                                                                 >  2:174031/1‑139 (MQ=255)        tACAGCGAGCTTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGattca                                                                                                                            <  2:719958/139‑1 (MQ=255)               aGCTTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGc                                                                                                                     >  1:315674/1‑139 (MQ=255)                  ttAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCcaa                                                                                                                  <  2:1482759/139‑1 (MQ=16)                    aGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCcaaca                                                                                                                >  2:65498/1‑139 (MQ=12)                       ttATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAAcc                                                                                                             >  2:495614/1‑139 (MQ=16)                        tATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                            <  2:716940/139‑1 (MQ=16)                          tGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcgcg                                                                                                          >  2:801615/1‑139 (MQ=17)                                                                      tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCcaa                                                                                                                  <  2:1430295/87‑1 (MQ=255)                                                                      tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCcaa                                                                                                                  >  1:1430295/1‑87 (MQ=255)                                                                                           cGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGcc                                                                                                                    >  1:308461/1‑64 (MQ=11)                                                                                           cGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGcc                                                                                                                    <  2:308461/64‑1 (MQ=11)                                                                                           cGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTg                                                    >  2:820467/1‑128 (MQ=11)                                                                                           cGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTg                                                    <  1:820467/128‑1 (MQ=11)                                                                                                cgcATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCcaa                                                                                                                  >  1:35856/1‑61 (MQ=11)                                                                                                cgcATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCcaa                                                                                                                  <  2:35856/61‑1 (MQ=255)                                                                                                cgcATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                            >  2:1222482/1‑67 (MQ=11)                                                                                                cgcATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                            <  1:1222482/67‑1 (MQ=11)                                                                                                cgcATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCAt                                                                                                       >  1:138683/1‑72 (MQ=255)                                                                                                cgcATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCAt                                                                                                       <  2:138683/72‑1 (MQ=11)                                                                                                cgcATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCTAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATg                                    >  2:973307/1‑139 (MQ=14)                                                                                                     cAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGat                                                                                                                               >  1:491428/1‑43 (MQ=255)                                                                                                     cAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGat                                                                                                                               <  2:491428/43‑1 (MQ=255)                                                                                                     cAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                            <  1:321109/62‑1 (MQ=11)                                                                                                     cAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                            >  2:321109/1‑62 (MQ=11)                                                                                                     cAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATgc                                   <  1:503668/135‑1 (MQ=255)                                                                                                     cAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATgc                                   >  2:503668/1‑135 (MQ=255)                                                                                                        gCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGa                            <  1:495614/139‑1 (MQ=17)                                                                                                                 gCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTAt                   <  1:973307/139‑1 (MQ=18)                                                                                                                  ccGCTGATCTGTGTCAGCGGTTACCGTGattcattt                                                                                                                         >  2:93979/1‑35 (MQ=255)                                                                                                                  ccGCTGATCTGTGTCAGCGGTTACCGTGattcattt                                                                                                                         <  1:93979/36‑2 (MQ=17)                                                                                                                        aTCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCt            <  2:920524/139‑1 (MQ=255)                                                                                                                             tgtCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTAt                   <  2:398865/127‑1 (MQ=17)                                                                                                                             tgtCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTAt                   >  1:398865/1‑127 (MQ=17)                                                                                                                             tgtCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGc              >  2:523443/1‑132 (MQ=18)                                                                                                                             tgtCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGc              <  1:523443/132‑1 (MQ=255)                                                                                                                                  gCGGTTACCGTGATTCATTTCTGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCa  >  2:568741/1‑139 (MQ=21)                                                                                                                                  gCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGa                                      <  2:310592/103‑1 (MQ=11)                                                                                                                                  gCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGa                                      >  1:310592/1‑103 (MQ=14)                                                                                                                                      |                                                                                                                                       ACTGGGTTACAGCGAGCTTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTCCTCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCA  >  NC_000913/357458‑357725

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑