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
A2 F60 I1 R1 12 89.5 3049092 98.9% 3015551 138.7

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.C95.2% 146.7 / ‑0.1 42coding (671/687 nt)rphtruncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base C (14/26);  total (15/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑CCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815742‑3816012
                                                                                                                                           |                                                                                                                                       
aaTAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑cc                                                                                                                                       >  1:41387/1‑140 (MQ=255)
 aTAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAATTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑ccc                                                                                                                                      >  1:89614/1‑140 (MQ=255)
 aTAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑ccc                                                                                                                                      >  1:949007/1‑140 (MQ=255)
    aaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAATTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACGATGGATTCGATT‑ccc‑cct                                                                                                                                  <  2:89614/140‑3 (MQ=255)
        ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGgattcgatt‑c                                                                                                                                        <  2:843537/131‑1 (MQ=255)
        ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGgattcgatt‑c                                                                                                                                        >  1:843537/1‑131 (MQ=255)
         gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGc                                                                                                                             >  1:1347533/1‑140 (MQ=255)
          cgcTGATATGGTTTCATGCCTTGGCTCCTCACCTTTCTTCTCTACAGAAAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGcc                                                                                                                            <  2:474232/140‑1 (MQ=255)
              gATATGGTTTCATGCCTTCGCTCCTCAACTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCagag                                                                                                                        <  2:1309320/140‑1 (MQ=255)
                    gTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCcaaca                                                                                                                  <  1:843825/140‑1 (MQ=255)
                      ttCATGCCTTCGCTCTTCATCTTACTTTTTTACAGACGAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAg                                                                                                                <  1:512865/140‑1 (MQ=255)
                         aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATg                                                                                                             >  2:97665/1‑140 (MQ=255)
                         aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATg                                                                                                             >  2:1230828/1‑140 (MQ=255)
                           gCCTTCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAg                                                                                                           <  2:1350449/140‑1 (MQ=255)
                              ttCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  1:1029620/140‑1 (MQ=255)
                              ttCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  1:107648/140‑1 (MQ=255)
                                cGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑CCC‑CATCGTGCGAGAGCCAACAAGATGAGTAGct                                                                                                      >  1:428462/1‑140 (MQ=255)
                                     ctcATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGACCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                 >  1:565650/1‑140 (MQ=255)
                                             aCTTTTCTACAGACAAA‑AAAAATGCGACTTATCAGTCCCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGaa                                                                                         <  1:512208/140‑1 (MQ=255)
                                             aCTTTTCTACAGAAAAATAAAAAGGCGACTCGTCAATCGTCTTAAAAAACAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGa                                                                                          <  2:552788/140‑1 (MQ=255)
                                                tttCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACgg                                                                                      <  1:275322/140‑1 (MQ=255)
                                                  tCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCt                                                                                    <  1:1210383/140‑1 (MQ=255)
                                                   cTACAGACAAA‑AAAACGGCGACCCAACAGCCGCCTTACAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTc                                                                                   <  1:426507/140‑1 (MQ=255)
                                                      cAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                                                                >  1:938688/1‑140 (MQ=255)
                                                        acaaaa‑aaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCtt                                                                              >  1:953556/4‑140 (MQ=255)
                                                           aaa‑aaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAAATGAGTAGCTCATCATGGGTGAACGGCTCGCCTTCTg                                                                           >  1:457947/1‑140 (MQ=255)
                                                             a‑aaaaaGGCGACTCATCAGTCGCCTTAAAAACCAGGTTGGCAGCGCCGTCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                                                         <  2:565650/140‑1 (MQ=255)
                                                                 gagacagACTCATCAGTCGCCTAAAAAATCAATTTCCCATCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc                                                                      <  2:637309/134‑1 (MQ=255)
                                                                   aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccc                                                                    <  1:1230828/140‑1 (MQ=255)
                                                                    ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                                                   <  2:1347533/140‑1 (MQ=255)
                                                                                   gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTATGCCGTCCCATGCACTTcctgtctc                                                    >  1:637309/1‑133 (MQ=255)
                                                                                    ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgc                                                   >  1:230717/1‑140 (MQ=255)
                                                                                      ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGTCTCGCCTCCTGGCGGCCCCTGCACTTCAATGATgcgc                                                 >  1:488656/1‑140 (MQ=255)
                                                                                       tAAAAATCAGTTTGCCATCGCCCCCTTCTGCGTCGATACGATGGATTCTATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGcc                                                <  2:488656/140‑1 (MQ=255)
                                                                                        aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGccc                                               <  1:1358920/140‑1 (MQ=255)
                                                                                                  ttGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtc                                     <  2:953556/140‑1 (MQ=255)
                                                                                                    gCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCTTCCCCTGCACTCCATTGATGCGCCCGTCTTCGGtcat                                   >  1:602793/1‑140 (MQ=255)
                                                                                                       aGCGCCGCCTTCTGCGTCGCTACAATGGATTGGATC‑CCCTC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                                <  2:457947/140‑1 (MQ=255)
                                                                                                       aGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                                <  1:66938/140‑1 (MQ=255)
                                                                                                        gcgcCGCCTTCTGCGGCGCTACTATTGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                               <  1:518838/140‑1 (MQ=255)
                                                                                                                   tGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCGCTGCACTTAAATTATGCGCCCGTCTTCGGTAATCACTACGTTCATGTc                    >  2:571576/1‑140 (MQ=255)
                                                                                                                    gCGTCGCTACAATCGATCCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCg                   <  2:1394062/140‑1 (MQ=255)
                                                                                                                        cGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGtct               >  2:127628/1‑140 (MQ=255)
                                                                                                                          cTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 >  1:1390839/1‑136 (MQ=255)
                                                                                                                          cTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 <  2:1390839/136‑1 (MQ=255)
                                                                                                                           tACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTg            <  2:949007/140‑1 (MQ=255)
                                                                                                                               aTGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGc        <  2:938688/140‑1 (MQ=255)
                                                                                                                                 ggATTCGATTCCCC‑C‑TCCGGCCCGAGCCAACAAGATGAGCAGCTCTTCTTGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCag      <  2:458979/140‑1 (MQ=255)
                                                                                                                                  gattcgattcCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 <  2:1059885/128‑1 (MQ=255)
                                                                                                                                  gattcgattcCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 >  1:1059885/1‑128 (MQ=255)
                                                                                                                                   attcgattcCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCagag    >  1:33686/1‑140 (MQ=255)
                                                                                                                                    ttcgattcCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCagag    >  1:1012296/1‑139 (MQ=255)
                                                                                                                                    ttcgattcCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCagag    <  2:1012296/139‑1 (MQ=255)
                                                                                                                                     tcgattcCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc  >  2:342891/1‑140 (MQ=255)
                                                                                                                                     tcgattcCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc  >  2:1280983/1‑140 (MQ=255)
                                                                                                                                     tcgattcCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGCTCATCACAACGATCGTGTCGGACTCTGCGGCAGAGTc  >  1:726426/1‑140 (MQ=255)
                                                                                                                                           |                                                                                                                                       
AATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAA‑AAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑CCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815742‑3816012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ 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