Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,478,503	(A)7→6	intergenic (+12/+47)	yjgN → / ← valS	hypothetical protein/valine tRNA synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,478,497	0	A	.	100.0%	310.0 / NA	68	intergenic (+6/+53)	yjgN/valS	hypothetical protein/valine tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (38/30);  total (38/30)

AGAACAACCAGATAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGATAAAAAAAGGCCGGATGCATGCTCCGGCCTTGCGTTTTCATCACTGTGTTTTGATTACAGCGCGGCGATAACAGC  >  NC_000913/4478422‑4478570                                                                            |                                                                          agaaCAACCAGATAAAGGCTTCTTAGCCAGTATTTCGCGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGATa                                                                           <  1:2230226/76‑1 (MQ=255) agaaCAACCAGATAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGATa                                                                           <  2:1200110/76‑1 (MQ=255) agaaCAACCAGATAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGATa                                                                           >  1:2091985/1‑76 (MQ=255)  gaaCAACCAGATAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGATaa                                                                          >  1:655204/1‑76 (MQ=255)      aacCAGATAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGATaaaaaa                                                                      <  2:1784670/76‑1 (MQ=255)      aacCAGATAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGATaaaaaa                                                                      <  2:3087932/76‑1 (MQ=255)       acCAGATAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGATaaaaaag                                                                     <  1:1835100/76‑2 (MQ=255)       acCAGATAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGATaaaaaag                                                                     <  1:3018734/76‑2 (MQ=255)        ccAGATAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGATaaaaaagg                                                                    <  1:5324655/76‑3 (MQ=255)         cAGATAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTCCCATTTCTGTAAGAGATaaaaaaggc                                                                   >  2:34984/1‑73 (MQ=255)         cAGATAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGATaaaaaaggc                                                                   >  2:2565569/1‑73 (MQ=255)         cAGATAAAGGCTTCTTAGCCAGCATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGATaaaaaaggc                                                                   >  2:435428/1‑73 (MQ=255)           gATAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCg                                                                <  1:5091183/76‑1 (MQ=255)             tAAAGGCTTCTTAGCCATTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGa                                                              <  1:1089051/76‑1 (MQ=255)             tAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGa                                                              <  2:3672127/76‑1 (MQ=255)             tAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGa                                                              <  2:1754977/76‑1 (MQ=255)              aaaGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGag                                                             <  2:180513/76‑2 (MQ=255)              aaaGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGag                                                             <  2:2234375/76‑2 (MQ=255)              aaaGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGag                                                             <  1:3827680/76‑2 (MQ=255)              aaaGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGag                                                             >  2:4824026/1‑75 (MQ=255)               aaGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGagc                                                            <  2:1783646/76‑3 (MQ=255)               aaGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGagc                                                            >  1:1506698/1‑74 (MQ=255)               aaGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGagc                                                            <  2:3427977/76‑3 (MQ=255)                   cttcttCGCCAGTATTTCACGGGGAGGGACTCCTACTTTACCATTTCTGTACGAGAT‑AAAAAAGGCCGga‑gcatgc                                                       <  1:2821555/76‑1 (MQ=255)                   cttcttAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGga‑gcatgc                                                       <  1:2839571/76‑1 (MQ=255)                    ttcttAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCt                                                      >  1:439378/1‑76 (MQ=255)                    ttcttAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCt                                                      >  2:535842/1‑76 (MQ=255)                     tcttAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTc                                                     >  2:4821635/1‑76 (MQ=255)                       ttAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCg                                                   <  2:4646920/76‑1 (MQ=255)                         aGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGc                                                 >  1:5121425/1‑76 (MQ=255)                            cAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCtt                                              >  2:3546508/1‑76 (MQ=255)                            cAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCtt                                              <  1:3496131/76‑1 (MQ=255)                            cAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCtt                                              <  1:2565569/76‑1 (MQ=255)                             aGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCttc                                             >  2:137594/1‑75 (MQ=255)                             aGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCttc                                             >  2:5280701/1‑75 (MQ=255)                             aGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCttc                                             <  1:5280702/76‑2 (MQ=255)                             aGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGG‑TGCATGCTCCGGCCttc                                             <  1:1613704/76‑2 (MQ=255)                              gTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCttcg                                            >  2:4199246/1‑74 (MQ=255)                              gTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCttcg                                            >  1:2613792/1‑74 (MQ=255)                              gTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCttcg                                            >  1:3323015/1‑74 (MQ=255)                              gTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCttcg                                            >  1:4238040/1‑74 (MQ=255)                               tATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCttcgt                                           <  1:25015/76‑4 (MQ=255)                                  ttCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGtttt                                       <  1:5637783/76‑1 (MQ=255)                                   tCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTtc                                      <  2:5424553/76‑1 (MQ=255)                                    cACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTtca                                     >  1:3126665/1‑76 (MQ=255)                                    cACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTtca                                     >  1:173447/1‑76 (MQ=255)                                     aCGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTtcat                                    <  2:2930857/76‑1 (MQ=255)                                      cGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTtcatc                                   <  2:1214992/76‑1 (MQ=255)                                      cGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTtcatc                                   <  2:2799004/76‑1 (MQ=255)                                       ggggAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTtcatca                                  >  2:445725/1‑76 (MQ=255)                                       ggggAGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTtcatca                                  >  2:110134/1‑76 (MQ=255)                                           aGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAACGGCCGGA‑GCATGCTCCGGCCTT‑CGTTGTCATCACtgt                              >  1:5565557/1‑76 (MQ=255)                                           aGTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACtgt                              >  1:5536370/1‑76 (MQ=255)                                            gTTATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACtgtg                             >  2:186423/1‑76 (MQ=255)                                             ttATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTgtgt                            >  2:2030042/1‑76 (MQ=255)                                              tATGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGtt                           >  1:2352476/1‑76 (MQ=255)                                                tGCCTTCTTTACCATTTTTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGtttt                         >  1:5651911/1‑76 (MQ=255)                                                tGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGtttt                         <  1:140896/76‑1 (MQ=255)                                                tGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGtttt                         >  2:1919643/1‑76 (MQ=255)                                                tGCCTTCTTTACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGtttt                         >  1:5716301/1‑76 (MQ=255)                                                       tttACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACa                  >  1:3581796/1‑76 (MQ=255)                                                        ttACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAg                 <  2:988408/76‑1 (MQ=255)                                                         tACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAgc                <  2:23312/76‑1 (MQ=255)                                                         tACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAgc                <  1:1436625/76‑1 (MQ=255)                                                         tACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAgc                <  2:4874901/76‑1 (MQ=255)                                                         tACCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAgc                >  2:1980049/1‑76 (MQ=255)                                                          aCCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAgcg               <  2:4360065/76‑1 (MQ=255)                                                          aCCATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAgcg               >  1:1974792/1‑76 (MQ=255)                                                           ccATTTCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAgcgc              <  2:3543240/76‑1 (MQ=255)                                                              tttCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAGCgcggc           >  1:3050028/1‑76 (MQ=255)                                                               ctCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCAGGCTCCGGCCTT‑CGTTTTCATGACTGTTTTTTTATTACAGCgcggcg          >  1:2313164/2‑76 (MQ=255)                                                                tCTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAGCGCGGCGa         <  2:4967062/76‑1 (MQ=255)                                                                 cTGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAGCGCGGCGAt        >  1:4810318/1‑76 (MQ=255)                                                                  tGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAGCGCGGCGATa       >  1:441915/1‑76 (MQ=255)                                                                  tGTAAGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGGTTTGATTACAGCGCGGCGATa       >  2:2919129/1‑76 (MQ=255)                                                                     aaGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAGCGCGGCGATAACa    >  2:1243197/1‑76 (MQ=255)                                                                     aaGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAGCGCGGCGATAACa    >  2:3093254/1‑76 (MQ=255)                                                                     aaGAGAT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAGCGCGGCGATAACa    >  1:2043116/1‑76 (MQ=255)                                                                       gagaT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTATAGCGCGGAGATAACAGc  >  1:3377699/1‑76 (MQ=255)                                                                       gagaT‑AAAAAAGGCCGGA‑GCATGCTCCGGCCTT‑CGTTTTCATCACTGTGTTTTGATTACAGCGCGGCGATAACAGc  >  1:2207485/1‑76 (MQ=255)                                                                            |                                                                          AGAACAACCAGATAAAGGCTTCTTAGCCAGTATTTCACGGGGAGTTATGCCTTCTTTACCATTTCTGTAAGAGATAAAAAAAGGCCGGATGCATGCTCCGGCCTTGCGTTTTCATCACTGTGTTTTGATTACAGCGCGGCGATAACAGC  >  NC_000913/4478422‑4478570

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑