Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,649,041	G→A	*73* (TAG→TAA)	ydfC →	uncharacterized protein, Qin prophage

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,649,041	0	G	A	100.0%	176.8 / NA	56	*73* (TAG→TAA)	ydfC	uncharacterized protein, Qin prophage
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (29/27);  total (29/27)

AGCGCAGGATCTGAAATGGGCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAGTAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAAAGTCAGACCATA  >  NC_000913/1648906‑1649176                                                                                                                                        |                                                                                                                                        aGCGCAGGATCTGAAATGGGCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTtaatag                                                                                                                                      <  2:214221/139‑1 (MQ=255)             gAAATGGGCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACaaa                                                                                                                          >  2:552540/1‑139 (MQ=255)                  gggCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTaa                                                                                                                     >  1:1103348/1‑139 (MQ=255)                  gggCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTaa                                                                                                                     >  2:1260488/1‑139 (MQ=255)                   ggCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATcaa                                                                                                                              <  1:1239156/129‑1 (MQ=255)                   ggCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATcaa                                                                                                                              >  2:1239156/1‑129 (MQ=255)                   ggCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAg                                                                                                                    >  2:80573/1‑139 (MQ=255)                   ggCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAg                                                                                                                    >  1:1358416/1‑139 (MQ=255)                    gCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAgg                                                                                                                   >  2:1206588/1‑139 (MQ=255)                    gCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAgg                                                                                                                   >  2:1651828/1‑139 (MQ=255)                     cTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGt                                                                                                                  >  1:196068/1‑139 (MQ=255)                        aTGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATcaac                                                                                                                             >  2:1225841/1‑125 (MQ=255)                        aTGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATcaac                                                                                                                             <  1:1225841/125‑1 (MQ=255)                         tGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGt                                                                                                              <  1:80573/139‑1 (MQ=255)                             gCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAAtt                                                                                                          >  1:1608159/1‑139 (MQ=255)                                        gCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTtctc                                                                                               <  2:1103348/139‑1 (MQ=255)                                           ggCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCAc                                                                                            <  2:196068/139‑1 (MQ=255)                                            gCTGAAAATCTGTCCGCTCTGGAGCAGGATCTCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTa                                                                                                                      <  1:1084912/112‑1 (MQ=255)                                            gCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATcaaca                                                                                                                            >  1:1343486/1‑106 (MQ=255)                                            gCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATcaaca                                                                                                                            <  2:1343486/106‑1 (MQ=255)                                            gCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCt                                                                                                                       >  2:264430/1‑111 (MQ=255)                                            gCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCt                                                                                                                       <  1:264430/111‑1 (MQ=255)                                            gCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCt                                                                                                                       <  2:1259712/111‑1 (MQ=255)                                            gCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCt                                                                                                                       >  1:1259712/1‑111 (MQ=255)                                            gCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTa                                                                                                                      >  2:1084912/1‑112 (MQ=255)                                            gCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTcc                                                                                              <  1:1413669/136‑1 (MQ=255)                                            gCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTcc                                                                                              >  2:1413669/1‑136 (MQ=255)                                            gCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACg                                                                                           >  2:1291081/1‑139 (MQ=255)                                               gAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGt                                                                                        <  2:1608159/139‑1 (MQ=255)                                                 aaaTCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAg                                                                                                               <  2:353094/114‑1 (MQ=255)                                                 aaaTCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAg                                                                                                               >  1:353094/1‑114 (MQ=255)                                                               tGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCt                                                                                                                       >  2:629218/1‑92 (MQ=255)                                                               tGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCt                                                                                                                       <  1:629218/92‑1 (MQ=255)                                                                             aCCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTg                                                          <  2:1358416/139‑1 (MQ=255)                                                                              ccAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTgc                                                         <  2:996413/139‑1 (MQ=255)                                                                                 aTCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAg                                                                                                    >  1:953709/1‑93 (MQ=255)                                                                                 aTCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAg                                                                                                    <  2:953709/93‑1 (MQ=255)                                                                                 aTCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGaca                                                                <  1:972872/129‑1 (MQ=255)                                                                                 aTCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGaca                                                                >  2:972872/1‑129 (MQ=255)                                                                                 aTCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGa                                                                  <  1:1210220/127‑1 (MQ=255)                                                                                 aTCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGa                                                                  >  2:1210220/1‑127 (MQ=255)                                                                                                       aaGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGa                                <  1:1651828/139‑1 (MQ=255)                                                                                                       aaGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGa                                <  1:552540/139‑1 (MQ=255)                                                                                                              gCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGata                         <  1:1206588/139‑1 (MQ=255)                                                                                                                       aTTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGt                                       >  2:342693/1‑116 (MQ=255)                                                                                                                       aTTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGt                                       <  1:342693/116‑1 (MQ=255)                                                                                                                         tACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACgg                                                                                          <  2:1628943/63‑1 (MQ=255)                                                                                                                         tACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACgg                                                                                          >  1:1628943/1‑63 (MQ=255)                                                                                                                                 cgcgTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAg                                                                                                    >  1:1720540/1‑45 (MQ=255)                                                                                                                                 cgcgTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAg                                                                                                    <  2:1720540/45‑1 (MQ=255)                                                                                                                                 cgcgTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGa                                <  1:727174/113‑1 (MQ=255)                                                                                                                                 cgcgTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGa                                >  2:727174/1‑113 (MQ=255)                                                                                                                                 cgcgTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAAAGTCa         <  2:763850/136‑1 (MQ=255)                                                                                                                                 cgcgTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAAAGTCa         >  1:763850/1‑136 (MQ=255)                                                                                                                                   cgTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGtgcgtgcg                                                                       <  2:887992/72‑1 (MQ=255)                                                                                                                                   cgTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGtgcgtgcg                                                                       >  1:887992/1‑72 (MQ=255)                                                                                                                                     ttAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAACGTCAGACCATa  >  2:1678852/1‑139 (MQ=255)                                                                                                                                        |                                                                                                                                        AGCGCAGGATCTGAAATGGGCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAGTAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAAAGTCAGACCATA  >  NC_000913/1648906‑1649176

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑