Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,648,375	T→C	intergenic (+34/‑133)	dicA → / → ydfA	Qin prophage; putative regulator for DicB/Qin prophage; uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,648,375	0	T	C	100.0%	260.5 / NA	74	intergenic (+34/‑133)	dicA/ydfA	Qin prophage; putative regulator for DicB/Qin prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (31/43);  total (31/43)

AAAAACTTCAATAAACTCTTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATTATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACGGTGTTCTCAGCAAACA  >  NC_000913/1648279‑1648469                                                                                                 |                                                                                               aaaaaCTTCAATAAACTCTTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATg                                                                                             <  2:592560/100‑1 (MQ=255)    agcTTAAATAAACTCTTTAAAGAATTACAAAAAGCCCGTAAGCGGACAAATAAAAGATATAATCAGCAACGAGGTAGCTTTTACCAAATCCATCATg                                                                                             <  2:151677/95‑1 (MQ=255)      cTTCAATAAACTCTTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGc                                                                                        >  2:296885/1‑100 (MQ=255)      cTTCAATAAACTCTTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGc                                                                                        >  1:1221901/1‑100 (MQ=255)      cTTCAATAAACTCTTTGAAGAATTACTAAAAGCCCGACAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGc                                                                                        >  1:919183/1‑100 (MQ=255)       ttCAATAAACTCTTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCt                                                                                       >  2:95325/1‑100 (MQ=255)        tCAATAAACTCTTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCta                                                                                      <  2:549731/100‑1 (MQ=255)          aaTAAACTCTTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCtata                                                                                    >  2:1163440/1‑100 (MQ=255)           aTAAACTCTTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAg                                                                                   >  2:1281026/1‑100 (MQ=255)            tAAACTCTTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGc                                                                                  <  2:164932/100‑1 (MQ=255)             aaaCTCTTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGc                                                                                  <  1:707071/99‑1 (MQ=255)             aaaCTCTTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCa                                                                                 >  1:869680/1‑100 (MQ=255)              aaCTCTTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCAt                                                                                <  1:1116100/100‑1 (MQ=255)                ctctTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCAt                                                                                <  1:873091/98‑1 (MQ=255)                ctctTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATAc                                                                              <  2:120200/100‑1 (MQ=255)                ctctTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATAc                                                                              <  1:549440/100‑1 (MQ=255)                 tctTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATACAAGATAACATCATCAATGAGTTATCTTTTACCACATCTATCATGTTAGCTATAGCATACa                                                                             <  2:106818/100‑1 (MQ=255)                  ctTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACaa                                                                            <  1:752475/100‑1 (MQ=255)                   tttGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACaaa                                                                           >  1:897828/1‑100 (MQ=255)                     tGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAAt                                                                         >  2:195142/1‑100 (MQ=255)                      gaagaaTTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATc                                                                        <  2:1255427/100‑1 (MQ=255)                      gaagaaTTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATc                                                                        >  1:182998/1‑100 (MQ=255)                        agaaTTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCAc                                                                      <  1:1285128/100‑1 (MQ=255)                          aaTTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACtt                                                                    <  1:296888/100‑1 (MQ=255)                            ttACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGa                                                                  <  2:733674/100‑1 (MQ=255)                              aCTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGAcc                                                                >  1:679873/1‑100 (MQ=255)                              aCTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGAcc                                                                <  2:748545/100‑1 (MQ=255)                               cTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGAcc                                                                >  2:930920/1‑99 (MQ=255)                                    aGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATg                                                          >  2:876706/1‑100 (MQ=255)                                      cccGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGtt                                                        <  2:1075881/100‑1 (MQ=255)                                       ccGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTa                                                       >  1:1198454/1‑100 (MQ=255)                                        cGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAg                                                      <  1:52672/100‑1 (MQ=255)                                        cGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAg                                                      <  1:1281037/100‑1 (MQ=255)                                           cAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCa                                                   >  1:919677/1‑100 (MQ=255)                                             gCGGACAAATAAAAGATAACATCATCAATTAGTTATCTTTTACCACATCAATCATGTCAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCa                                                   >  2:913798/1‑98 (MQ=255)                                             gCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATg                                                 <  2:601828/100‑1 (MQ=255)                                             gCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATg                                                 <  1:1009177/100‑1 (MQ=255)                                              cGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATgg                                                <  1:238691/100‑1 (MQ=255)                                              cGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATgg                                                >  2:456922/1‑100 (MQ=255)                                              cGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATgg                                                <  1:699149/100‑1 (MQ=255)                                               ggACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGc                                               <  2:427607/100‑1 (MQ=255)                                                gACAAATCAGAGATAACGTCATCTAAGAGTTATTTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCagg                                                 <  2:1065061/97‑3 (MQ=255)                                                    aaTAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATc                                          >  2:1156470/1‑100 (MQ=255)                                                     aTAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCt                                         <  2:220217/100‑1 (MQ=255)                                                     aTAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCt                                         >  2:52335/1‑100 (MQ=255)                                                     aTAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCt                                         >  1:302822/1‑100 (MQ=255)                                                      tAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCtt                                        >  2:839630/1‑100 (MQ=255)                                                      tAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCtt                                        >  1:752805/1‑100 (MQ=255)                                                         aaGATAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGtt                                     >  2:1057825/1‑100 (MQ=255)                                                           gATAACATCATCAATGAGTTATCTTTTACCACATCAATCATATTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTg                                   >  1:421643/1‑100 (MQ=255)                                                             tAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCa                                 <  2:919175/100‑1 (MQ=255)                                                             tAACATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCa                                 <  1:280738/100‑1 (MQ=255)                                                               aCATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTTCAt                                >  1:53551/1‑99 (MQ=255)                                                               aCATCATCAATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATc                               <  1:1166774/100‑1 (MQ=255)                                                                  tcatcaATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAac                            <  2:897821/100‑1 (MQ=255)                                                                  tcatcaATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAac                            <  1:424433/100‑1 (MQ=255)                                                                   catcaATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAaca                           <  2:981428/100‑1 (MQ=255)                                                                    atcaATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAacac                          <  2:741332/100‑1 (MQ=255)                                                                      caATGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAacacac                        >  1:178986/1‑100 (MQ=255)                                                                        aTGAGTTATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCg                      >  1:778686/1‑100 (MQ=255)                                                                             ttATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACgg                 <  1:850213/100‑1 (MQ=255)                                                                             ttATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACgg                 >  2:850207/1‑100 (MQ=255)                                                                              tATCTTTTACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACGgt                <  1:960522/100‑1 (MQ=255)                                                                                  ttttACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACGGTGTtc            <  1:213946/100‑1 (MQ=255)                                                                                  ttttACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACGGTGTtc            <  2:869674/100‑1 (MQ=255)                                                                                    ttACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGTGCGgtgtgttg          <  1:95327/100‑5 (MQ=255)                                                                                     tACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACGGTGTTCTCa         <  1:1061347/100‑1 (MQ=255)                                                                                     tACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACGGTGTTCTCa         >  2:773316/1‑100 (MQ=255)                                                                                     tACCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACGGTGTTCTCa         >  2:663873/1‑100 (MQ=255)                                                                                      aCCACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACGGTGTTCTCAg        <  1:195144/100‑1 (MQ=255)                                                                                       ccACATCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACGGTGTTCTCAGc       >  2:943054/1‑100 (MQ=255)                                                                                          caTCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCACACGGTGTTCTCAGCaaa    <  2:706743/100‑1 (MQ=255)                                                                                           atcaatcaTGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACGGTGTTCTCAGCAAAc   <  2:1229968/100‑1 (MQ=255)                                                                                            tCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACGGTGTTCTCAGCAAACa  <  2:486668/100‑1 (MQ=255)                                                                                            tCAATCATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACGGTGTTCTCAGCAAACa  <  2:486841/100‑1 (MQ=255)                                                                                                 |                                                                                               AAAAACTTCAATAAACTCTTTGAAGAATTACTAAAAGCCCGTCAGCGGACAAATAAAAGATAACATCATCAATGAGTTATCTTTTACCACATCAATTATGTTAGCTATAGCATACAAAATCACTTGACCGATATGTTAGTCATGGCTAATCTTGTTTGCATCAACACACCGCACGGTGTTCTCAGCAAACA  >  NC_000913/1648279‑1648469

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑