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 I1 R1 99 64.8 3148104 96.3% 3031624 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,712,518 (C)6→5 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.92.5% 216.1 / 16.2 54intergenic (+355/‑256)nth/dtpADNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
Reads supporting (aligned to +/- strand):  ref base C (3/1);  new base . (27/22);  total (30/24)
Fisher's exact test for biased strand distribution p-value = 6.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

ATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTC  >  NC_000913/1712415‑1712607
                                                                                                  |                                                                                              
atTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCAcc                                                                                               >  2:955938/1‑100 (MQ=255)
   gACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCAccccc                                                                                            <  2:796710/100‑1 (MQ=255)
   gACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAACAGCAGAACATATCGCCGTTAAGCCATCAccccc                                                                                            >  2:1525760/1‑100 (MQ=255)
    aCCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCAccccct                                                                                           <  2:992469/100‑2 (MQ=255)
     ccTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCAccccctc                                                                                          >  1:495756/1‑98 (MQ=255)
     ccTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCAccccctc                                                                                          >  2:484769/1‑98 (MQ=255)
       tACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCAccccctctc                                                                                        >  1:466281/1‑96 (MQ=255)
        aCAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTca                                                                                      >  1:1533893/1‑100 (MQ=255)
        aCAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTca                                                                                      >  1:887343/1‑100 (MQ=255)
        aCAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTca                                                                                      >  1:99754/1‑100 (MQ=255)
          aaaaCATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTcagt                                                                                    >  2:993241/1‑100 (MQ=255)
           aaaCATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTcagtg                                                                                   <  1:484772/100‑1 (MQ=255)
            aaCATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTcagtgc                                                                                  <  1:16474/100‑1 (MQ=255)
            aaCATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTcagtgc                                                                                  <  1:364776/100‑1 (MQ=255)
                         cTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCt                                                                     >  2:626286/1‑100 (MQ=255)
                          tATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTg                                                                    >  2:9844/1‑100 (MQ=255)
                            tttttCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGcc                                                                  <  1:158816/100‑1 (MQ=255)
                             ttttCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCg                                                                 >  1:1553649/1‑100 (MQ=255)
                              tttCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGt                                                                <  1:1488318/100‑1 (MQ=255)
                               ttCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGtt                                                               >  2:1264120/1‑100 (MQ=255)
                               ttCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGtt                                                               >  2:429756/1‑100 (MQ=255)
                               ttCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGtt                                                               >  2:1143174/1‑100 (MQ=255)
                                tCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTa                                                              <  1:869689/100‑1 (MQ=255)
                                tCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTa                                                              >  2:554889/1‑100 (MQ=255)
                                 cAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTAc                                                             >  1:1081636/1‑100 (MQ=255)
                                 cAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTAc                                                             >  2:1539124/1‑100 (MQ=255)
                                  aGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTAc                                                             >  1:187737/1‑100 (MQ=255)
                                      aCTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGttt                                                         >  2:460354/1‑100 (MQ=255)
                                       cTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGttttt                                                       >  1:634401/1‑100 (MQ=255)
                                       cTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGttttt                                                       >  1:264605/1‑100 (MQ=255)
                                       cTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGttttt                                                       >  2:363152/1‑100 (MQ=255)
                                         ggACTCTCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGttttt                                                       >  2:1352475/1‑98 (MQ=255)
                                         ggACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTg                                                     <  2:534108/100‑1 (MQ=255)
                                         ggACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTg                                                     >  1:1321814/1‑100 (MQ=255)
                                          gACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGa                                                    <  1:126762/100‑1 (MQ=255)
                                             tATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGCGCAGTGAAAAAATCTGCCGTTACGTTTTTTGaaaa                                                 <  2:1077774/100‑1 (MQ=255)
                                                  cACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAAttt                                             >  1:809500/1‑100 (MQ=255)
                                                  cACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAAttt                                             <  1:91428/100‑1 (MQ=255)
                                                  cACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTa                                            >  1:1117637/1‑100 (MQ=255)
                                                    cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAAc                                          <  2:1330730/100‑1 (MQ=255)
                                                    cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAAc                                          >  2:162616/1‑100 (MQ=255)
                                                             aCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATaa                                 <  1:162616/100‑1 (MQ=255)
                                                               gCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTAAGAAAATTAAAAAATTTAACGCTGGATAACa                               <  2:1068025/100‑1 (MQ=255)
                                                                   aaTAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTc                           <  1:888542/100‑1 (MQ=255)
                                                                     tAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTccc                         >  2:1479379/1‑100 (MQ=255)
                                                                       gCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCgg                       <  1:57086/100‑1 (MQ=255)
                                                                       gCAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCgg                       <  1:993249/100‑1 (MQ=255)
                                                                        cAGAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCgg                       >  2:1263454/1‑99 (MQ=255)
                                                                          gAACATATCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAAt                    >  1:695220/1‑100 (MQ=255)
                                                                               tatCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTg               <  1:686549/100‑1 (MQ=255)
                                                                               tatCGCCGTTAAGCCATCA‑CCCCCGCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTg               <  2:1081629/100‑1 (MQ=255)
                                                                                 tCGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGaa             <  2:99754/100‑1 (MQ=255)
                                                                                 tCGCCGTTAAGCCATC‑TCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGaa             <  2:1533883/100‑1 (MQ=255)
                                                                                  cGCCGTTAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAAt            >  2:469410/1‑100 (MQ=255)
                                                                                  cGCCGATAAGCCATCA‑CCCCCTCTCAGAGCAGAGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGaa             <  2:887335/99‑1 (MQ=255)
                                                                                       ttAAGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTcccc       <  1:643009/100‑1 (MQ=255)
                                                                                         aaGCCAGCA‑CCCCCTCACAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCg      <  1:1176163/99‑1 (MQ=255)
                                                                                          aGCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAATTTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc    >  2:284536/1‑100 (MQ=255)
                                                                                           gCCATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt   >  1:804791/1‑100 (MQ=255)
                                                                                            ccATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTc  >  2:416754/1‑100 (MQ=255)
                                                                                            ccATCA‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTc  <  2:317539/100‑1 (MQ=255)
                                                                                                  |                                                                                              
ATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTC  >  NC_000913/1712415‑1712607

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A