Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A22 F60 I1 R1 20 69.2 2499260 99.0% 2474267 138.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,815,8791.C93.6% 166.1 / 3.4 47coding (671/687 nt)rphtruncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (1/2);  new base C (20/24);  total (21/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.55e-01

AACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑C‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCT  >  NC_000913/3815746‑3816013
                                                                                                                                       |                                                                                                                                       
aaCTGGCGCTGATATTGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑c‑cccct                                                                                                                                  <  2:313807/140‑3 (MQ=255)
aaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑c‑cccct                                                                                                                                  <  1:466634/140‑3 (MQ=255)
   tGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑c‑cccctcgg                                                                                                                               >  1:208461/1‑135 (MQ=255)
   tGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑CACCCTCgg                                                                                                                                >  2:729033/1‑140 (MQ=255)
    ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCggg                                                                                                                               <  1:1129767/140‑1 (MQ=255)
    ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCggg                                                                                                                               >  1:373177/1‑140 (MQ=255)
    ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCggg                                                                                                                               >  2:968635/1‑140 (MQ=255)
          gATATGGTTTCATGCCTTCGGTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATCC‑C‑CCCTCGGGCCagag                                                                                                                         <  2:1046362/140‑1 (MQ=255)
             atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCca                                                                                                                      >  2:833915/1‑140 (MQ=255)
               ggTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCcaac                                                                                                                    <  2:410210/140‑1 (MQ=255)
                gTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCcaaca                                                                                                                   >  1:488085/1‑140 (MQ=255)
                     aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATg                                                                                                              >  2:1235/1‑140 (MQ=255)
                           tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGc                                                                                                        <  1:202309/140‑1 (MQ=255)
                            cGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATg                                                                                                              >  2:779232/1‑133 (MQ=255)
                            cGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATg                                                                                                              <  1:779232/133‑1 (MQ=255)
                            cGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGct                                                                                                       >  2:1178699/1‑140 (MQ=255)
                                       ttACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTg                                                                                            <  2:377340/140‑1 (MQ=255)
                                         aCTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGaa                                                                                          >  1:533132/1‑140 (MQ=255)
                                              tCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGct                                                                                                       >  1:867421/1‑122 (MQ=255)
                                              tCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGct                                                                                                       <  2:867421/122‑1 (MQ=255)
                                              tCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCt                                                                                     >  2:172132/1‑140 (MQ=255)
                                               cTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑CACCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTc                                                                                    <  1:729033/140‑1 (MQ=255)
                                                  cAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                                                                 >  2:501115/1‑140 (MQ=255)
                                                     aCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTc                                                                              >  1:722175/1‑140 (MQ=255)
                                                            aaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc                                                                       <  1:1152235/140‑1 (MQ=255)
                                                               ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                                                    <  1:1235/140‑1 (MQ=255)
                                                                 cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                  <  1:862197/140‑1 (MQ=255)
                                                                   aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCa                                                                >  2:478873/1‑140 (MQ=255)
                                                                   aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCa                                                                <  2:208461/140‑1 (MQ=255)
                                                                   aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCa                                                                <  2:333225/140‑1 (MQ=255)
                                                                         caGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCaa                                                          <  1:501115/140‑1 (MQ=255)
                                                                              gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgatg                                                     >  2:524671/1‑140 (MQ=255)
                                                                                 ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                  >  1:166272/1‑140 (MQ=255)
                                                                                 ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                  >  2:31551/1‑140 (MQ=255)
                                                                                       aTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                            <  1:1203812/140‑1 (MQ=255)
                                                                                       aTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                            <  1:524671/140‑1 (MQ=255)
                                                                                         cAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTc                                          <  1:1178699/140‑1 (MQ=255)
                                                                                          aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                         >  1:810401/1‑140 (MQ=255)
                                                                                            tttGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                                       <  2:810401/140‑1 (MQ=255)
                                                                                               gCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                                    >  2:372663/1‑140 (MQ=255)
                                                                                                 cAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcatca                                  <  1:362827/140‑1 (MQ=255)
                                                                                                   gcgcCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                                <  1:172132/140‑1 (MQ=255)
                                                                                                      ccgccTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTTAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCCCCCGTCTTCGGTCATCACTACg                             >  1:601522/1‑140 (MQ=255)
                                                                                                       cgccTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGt                            <  1:372663/140‑1 (MQ=255)
                                                                                                       cgccTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGt                            <  2:533132/140‑1 (MQ=255)
                                                                                                              tGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTc                     >  2:819660/1‑140 (MQ=255)
                                                                                                               gCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCg                    <  1:968635/140‑1 (MQ=255)
                                                                                                                 gTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                  <  2:1242015/140‑1 (MQ=255)
                                                                                                                           tGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTTAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa        <  2:601522/140‑1 (MQ=255)
                                                                                                                            ggATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCag       <  1:783208/140‑1 (MQ=255)
                                                                                                                             gattcgat‑tcC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga      >  1:71424/1‑140 (MQ=255)
                                                                                                                                tcgat‑tcC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc   >  1:457050/1‑140 (MQ=255)
                                                                                                                                 cgat‑tcC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCt  <  1:1237007/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                       
AACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑C‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCT  >  NC_000913/3815746‑3816013

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A