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
A11 F142 I0 R1 175 91.2 4812830 94.5% 4548124 99.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,712,518 (C)6→5 100% intergenic (+360/‑251) nth → / → dtpA DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,712,5130C.95.3% 277.8 / 7.1 64intergenic (+355/‑256)nth/dtpADNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
Reads supporting (aligned to +/- strand):  ref base C (2/1);  new base . (30/31);  total (32/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.08e-01

TATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCT  >  NC_000913/1712414‑1712606
                                                                                                   |                                                                                              
tatTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCAc                                                                                                >  1:1718538/1‑100 (MQ=255)
      ccTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCAccccctc                                                                                          <  1:162491/100‑3 (MQ=255)
       ctaacacaCAATACACTGTCTATTTTTCATTAAATGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATTTTCGGTAAGCCATAAcaccctt                                                                                          <  2:802380/92‑3 (MQ=255)
        tACAAAACATTACACTGGCTATTTTTTTTTTTTTTTACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCAccccctctc                                                                                        >  2:1793480/1‑96 (MQ=255)
        tACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATGTCGCCGTTAAGCCATCAccccctctc                                                                                        <  1:1458161/100‑5 (MQ=255)
        tACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCAccccctctc                                                                                        >  1:1962430/1‑96 (MQ=255)
        tACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCAccccctctc                                                                                        <  1:1772452/100‑5 (MQ=255)
         aCAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTca                                                                                      >  1:1355826/1‑100 (MQ=255)
         aCAAAACATTACACTGGCTATTTATCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTca                                                                                      >  2:195638/1‑100 (MQ=255)
          cAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTcag                                                                                     <  1:103449/100‑1 (MQ=255)
           aaaaCATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTcagt                                                                                    >  2:1989375/1‑100 (MQ=255)
            aaaCATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTcagtg                                                                                   >  2:1733493/1‑100 (MQ=255)
            aaaCATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTcagtg                                                                                   <  1:1844964/100‑1 (MQ=255)
            aaaCATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTcagt                                                                                    >  2:201586/1‑99 (MQ=255)
            aaaCATTACACTGGCTATTTATCAAAAACTGGACTAACTCACTAGTAAAAACGCTAAATACCAGCACATATCACCGATAAGCCATCA‑CCCCCTCTca                                                                                      >  2:768186/1‑97 (MQ=255)
              aCATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTcagtgca                                                                                 <  1:2337865/100‑1 (MQ=255)
               cATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTcagtgcag                                                                                <  1:2103435/100‑1 (MQ=255)
                aTTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCTCTcagtgcag                                                                                <  1:1858552/100‑1 (MQ=255)
                  tACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCTCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGa                                                                             <  2:1559299/100‑1 (MQ=255)
                    cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGaaa                                                                           >  1:1930973/1‑100 (MQ=255)
                    cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGaaa                                                                           >  1:9237/1‑100 (MQ=255)
                      cTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACGTAACGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGaaaaa                                                                         >  2:1684702/1‑100 (MQ=255)
                       tGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGaaaaaa                                                                        <  1:1959831/100‑1 (MQ=255)
                        ngCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAAt                                                                       >  2:2317246/2‑100 (MQ=255)
                        ggCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAAt                                                                       >  2:1969901/1‑100 (MQ=255)
                         gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATc                                                                      <  1:1939501/100‑1 (MQ=255)
                          cTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCt                                                                     >  1:37650/1‑100 (MQ=255)
                           tATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTg                                                                    <  1:782558/100‑1 (MQ=255)
                              ttttCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGcc                                                                  >  2:582084/1‑99 (MQ=255)
                              ttttCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCg                                                                 >  2:1335214/1‑100 (MQ=255)
                                  cAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTAc                                                             >  1:70743/1‑100 (MQ=255)
                                   aGAAACTGGATTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑TCCCCTCTCTGTGCAGTGAAAAAATCTGCCGTTACg                                                            <  2:1028608/100‑1 (MQ=255)
                                      aaCTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑ttt                                                        >  2:825656/1‑100 (MQ=255)
                                      aaCTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CACCCTCTCAGTACAGTGAAAAAATCTGCCGTTACG‑ttt                                                        >  2:948327/1‑100 (MQ=255)
                                         tGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑tttttt                                                     <  1:756991/100‑1 (MQ=255)
                                         tGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑tttttt                                                     <  1:167163/100‑1 (MQ=255)
                                         tGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑tttttt                                                     >  1:2388947/1‑100 (MQ=255)
                                         tGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑tttttt                                                     <  2:1116774/100‑1 (MQ=255)
                                            aCTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTg                                                    <  1:1277184/98‑1 (MQ=255)
                                            aCTATCTCACTAGAAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTg                                                    <  2:1341684/98‑1 (MQ=255)
                                              tATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGaaa                                                 >  2:550263/1‑100 (MQ=255)
                                                    aCTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTaa                                          <  2:242174/100‑1 (MQ=255)
                                                     cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTa                                           <  1:1373644/98‑1 (MQ=255)
                                                     cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAAc                                         >  2:5229/1‑100 (MQ=255)
                                                          aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTTAAAAAATTTAACGTTg                                     >  2:447635/1‑100 (MQ=255)
                                                           aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGa                                   >  2:1031806/1‑100 (MQ=255)
                                                            aaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCtag                                    >  2:907908/1‑97 (MQ=255)
                                                               cGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGTAAATTTTAACGCTGGATAAc                               >  2:2167346/1‑100 (MQ=255)
                                                               cGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAAc                               <  2:1410412/100‑1 (MQ=255)
                                                               cGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAAc                               <  1:5229/100‑1 (MQ=255)
                                                               cGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAAc                               <  2:217516/100‑1 (MQ=255)
                                                                gCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACa                              <  2:2190379/100‑1 (MQ=255)
                                                                 cTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACAt                             >  1:2144599/1‑100 (MQ=255)
                                                                  tAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACAt                             <  1:976932/99‑1 (MQ=255)
                                                                      tAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTccc                        >  2:1655275/1‑100 (MQ=255)
                                                                       aGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCCCg                       <  2:1345175/100‑1 (MQ=255)
                                                                        gCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCCCgg                      <  1:1684722/100‑1 (MQ=255)
                                                                        gCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCCCgg                      <  1:730657/100‑1 (MQ=255)
                                                                           gAACATATCGACGTTAATCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAAt                   <  2:2020748/100‑1 (MQ=255)
                                                                              cATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGt                <  1:1048322/100‑1 (MQ=255)
                                                                                 atCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGa             <  2:1967774/100‑1 (MQ=255)
                                                                                  tCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGaa            >  1:2140382/1‑100 (MQ=255)
                                                                                    gCCGTTAAGCCATCA‑CCACCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAAAGCTGGATAACATTTCCCGGAATGGTTGAAtt          >  2:1520255/1‑100 (MQ=255)
                                                                                        ttAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTcccc      >  1:1550745/1‑100 (MQ=255)
                                                                                        ttAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTcccc      <  1:1031817/100‑1 (MQ=255)
                                                                                        ttAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCAGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTTCCGGAATGGTTGAATTccc       <  2:795638/99‑1 (MQ=255)
                                                                                         tAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCg     <  1:825665/100‑1 (MQ=255)
                                                                                          aaGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc    >  1:246236/1‑100 (MQ=255)
                                                                                            gCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTTTTTTTTTTTTCTCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt  >  2:1773610/1‑100 (MQ=255)
                                                                                            gCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCTCTGAATGGTTGAATTCCCCGcc   <  2:930726/99‑1 (MQ=255)
                                                                                            gCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCACGCCt  >  1:118134/1‑100 (MQ=255)
                                                                                                   |                                                                                              
TATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACG‑TTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCT  >  NC_000913/1712414‑1712606

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A