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 15 55.1 2015454 99.1% 1997314 138.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,172,920 G→A A131T (GCC→ACC)  mdaB → NADPH:quinone oxidoreductase MdaB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,172,9200GA97.8% 145.7 / ‑4.0 45A131T (GCC→ACC) mdaBNADPH:quinone oxidoreductase MdaB
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (27/17);  total (28/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

CGAAGGTCACGGGACGCTGTATGCCAGCGATGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAGCCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGCCGACATTTATCGCTAATGACGTGATAAAAATGCC  >  NC_000913/3172790‑3173053
                                                                                                                                  |                                                                                                                                     
cGAAGGTCACGGGACGCTGTATGCCAGCGATGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCg                                                                                                                              >  2:816889/1‑140 (MQ=255)
  aaGGTCACGGGACGCTGTATGCCAGCGATGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGaa                                                                                                                            >  2:641233/1‑140 (MQ=255)
     gTCACGGGACGCTGTATGCCAGCGATGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTCCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGaaaaa                                                                                                                         >  1:351604/1‑140 (MQ=255)
      tCACGGGACGCTGTATGCCAGCGATGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAg                                                                                                                        >  2:233897/1‑140 (MQ=255)
            gACGCTGTATGCCAGCGATGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGt                                                                                                                  >  2:387375/1‑140 (MQ=255)
                cTGTATGCCAGCGATGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGttctt                                                                                                              >  2:643552/1‑140 (MQ=255)
                   tATGCCAGCGATGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCa                                                                                                           <  1:816889/140‑1 (MQ=255)
                    aTGCCAGCGATGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCAc                                                                                                          >  2:781051/1‑140 (MQ=255)
                        cAGCGATGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTCCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACggcg                                                                                                      <  2:351604/140‑1 (MQ=255)
                           cGATGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACggcgttg                                                                                                   >  2:779526/1‑140 (MQ=255)
                           cGATGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACggcgttg                                                                                                   >  1:101633/1‑140 (MQ=255)
                            gATGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACggcgttgg                                                                                                  <  1:146374/140‑1 (MQ=255)
                             aTGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAGCCTTCACCGAAAAAGATCAGTTCTTCCACggcgttggc                                                                                                 >  2:741304/1‑140 (MQ=255)
                             aTGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACggcgttggc                                                                                                 >  1:416934/1‑140 (MQ=255)
                                     aCCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACgg                                                                                         <  1:643552/140‑1 (MQ=255)
                                     aCCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACgg                                                                                         <  2:101633/140‑1 (MQ=255)
                                     aCCCACAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACgg                                                                                         >  2:696674/1‑140 (MQ=255)
                                       ccGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGgtg                                                                                       <  1:641233/140‑1 (MQ=255)
                                               aTCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTg                                                                               <  1:779526/140‑1 (MQ=255)
                                               aTCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTg                                                                               <  1:233897/140‑1 (MQ=255)
                                                  cGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCg                                                                            <  2:237082/140‑1 (MQ=255)
                                                             tACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGc                                                                 >  2:484349/1‑140 (MQ=255)
                                                                  ttCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAAcc                                                            <  1:696674/140‑1 (MQ=255)
                                                                                     ggCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCt                                                     >  1:724792/1‑128 (MQ=255)
                                                                                     ggCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCt                                                     <  2:724792/128‑1 (MQ=255)
                                                                                     ggCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCg                                                   >  1:629854/1‑130 (MQ=255)
                                                                                     ggCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCg                                                   <  2:629854/130‑1 (MQ=255)
                                                                                     ggCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAAcc                                         >  2:239539/1‑140 (MQ=255)
                                                                                     ggCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAAcc                                         >  1:21396/1‑140 (MQ=255)
                                                                                       cAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGc                                       >  1:74979/1‑140 (MQ=255)
                                                                                          aaaaTATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCg                                                   <  2:738185/125‑1 (MQ=255)
                                                                                          aaaaTATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCg                                                   >  1:738185/1‑125 (MQ=255)
                                                                                          aaaaTATATGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGc                                    >  1:337167/1‑140 (MQ=255)
                                                                                              tatatGCTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGCCGAc                                <  2:382787/140‑1 (MQ=255)
                                                                                                    cTTTCTCTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGCCGACATTTAt                          <  2:343823/140‑1 (MQ=255)
                                                                                                       tctcTGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGATGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGCCGACATTTATCGc                       >  2:641297/1‑140 (MQ=255)
                                                                                                         tctGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGCCGACATTTa                           >  2:147251/1‑134 (MQ=255)
                                                                                                         tctGACCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGCCGACATTTa                           <  1:147251/134‑1 (MQ=255)
                                                                                                             aCCTGGAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGCCGACATTTATCGCTAATGa                 >  2:13613/1‑140 (MQ=255)
                                                                                                                 ggAACGCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGCCGACATTTATCGCTAATGACGTg             >  2:940201/1‑140 (MQ=255)
                                                                                                                      gCACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGCCGACATTTATCGCTAATGACGTGATaaa        <  1:239539/140‑1 (MQ=255)
                                                                                                                       cACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGTTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGCCGACATTTATCGCTAATGACGTGATaaaa       >  1:339378/1‑140 (MQ=255)
                                                                                                                       cACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGCCGACATTTATCGCTAATGACGTGATaaaa       >  2:613791/1‑140 (MQ=255)
                                                                                                                       cACCAATGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGCCGACATTTATCGCTAATGACGTGATaaaa       >  2:742982/1‑140 (MQ=255)
                                                                                                                            aTGGAAACCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGCCGACATTTATCGCTAATGACGTGATAAAAATGcc  >  1:371830/1‑140 (MQ=255)
                                                                                                                                  |                                                                                                                                     
CGAAGGTCACGGGACGCTGTATGCCAGCGATGGTCGTACCCGCAAAGATCCGTCGAAAAAATACGGTTCCGGCGGCCTGGTACAGGGCAAAAAATATATGCTTTCTCTGACCTGGAACGCACCAATGGAAGCCTTCACCGAAAAAGATCAGTTCTTCCACGGCGTTGGCGTTGACGGTGTGTATCTGCCGTTCCATAAAGCAAACCAATTCCTCGGTATGGAACCGCTGCCGACATTTATCGCTAATGACGTGATAAAAATGCC  >  NC_000913/3172790‑3173053

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