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
A25 F36 I0 R2 1302 104.9 4551290 96.3% 4382892 111.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 884,868 T→A 7.0% L399* (TTA→TAA)  mdfA → multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913884,8680TA 7.0% 200.0 / 5.3 57L399* (TTA→TAA) mdfAmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base T (26/27);  new base A (2/2);  total (28/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.44e-01

TGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTTGTGCGATCAGGCATTCTCGAATTAATGGTGATGGTCGTCAAT  >  NC_000913/884736‑884966
                                                                                                                                    |                                                                                                  
tgctgcAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGAt                                                                                     <  3:796837/148‑1 (MQ=255)
    gcAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGa                                                                                 >  2:203283/1‑148 (MQ=255)
    gcAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTAAAAAGATaa                                                                                           >  2:652362/1‑138 (MQ=255)
    gcAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTAAAAAGATaa                                                                                           <  1:652362/138‑1 (MQ=255)
              aTCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACg                                                                       >  3:868536/1‑148 (MQ=255)
                 tttACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAg                                                                    <  4:868536/148‑1 (MQ=255)
                 tttACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAg                                                                    <  1:203283/148‑1 (MQ=255)
                    aCCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGaa                                                                     <  3:127156/144‑1 (MQ=255)
                    aCCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGaa                                                                     >  4:127156/1‑144 (MQ=255)
                     ccGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTGATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATaa                                                                                           >  2:916793/1‑121 (MQ=255)
                     ccGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCGTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATaa                                                                                           <  1:916793/121‑1 (MQ=255)
                         tGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAg                                                                    <  1:67796/140‑1 (MQ=255)
                         tGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAg                                                                    >  2:67796/1‑140 (MQ=255)
                         tGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTaaaaa                                                            >  3:52448/1‑148 (MQ=255)
                                  aaTCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTaaa                                                                                                 >  2:160180/1‑102 (MQ=255)
                                  aaTCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTaaa                                                                                                 <  1:160180/102‑1 (MQ=255)
                                    tCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTAAAAAGATa                                                                                            >  4:298111/1‑105 (MQ=255)
                                    tCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTAAAAAGATa                                                                                            <  3:298111/105‑1 (MQ=255)
                                        cAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGAt                                                                                     <  2:1075634/108‑1 (MQ=255)
                                        cAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGAt                                                                                     >  1:1075634/1‑108 (MQ=255)
                                          aaCATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGAt                                                                                             >  1:968200/1‑98 (MQ=255)
                                          aaCATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGAt                                                                                             <  2:968200/98‑1 (MQ=255)
                                           aCATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTtgt                                          <  4:52448/148‑1 (MQ=255)
                                           aCATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTtgt                                          >  4:607124/1‑148 (MQ=255)
                                            cATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTaaaaaaa                                                          >  3:880833/1‑131 (MQ=255)
                                            cATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTaaaaaaa                                                          <  4:880833/131‑1 (MQ=255)
                                            cATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTtgtg                                         >  3:469674/1‑148 (MQ=255)
                                                   ggCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGAt                                                                                     >  1:122886/1‑97 (MQ=255)
                                                   ggCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGAt                                                                                     <  2:122886/97‑1 (MQ=255)
                                                       gAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATtctc                                                                          <  4:537164/104‑1 (MQ=255)
                                                       gAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATtctc                                                                          >  3:537164/1‑104 (MQ=255)
                                                                 aaCGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTTGTGCGATCAGGCATTCTCGAATTa                    <  3:607124/148‑1 (MQ=255)
                                                                           ttAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGa                                                                                      <  1:184111/72‑1 (MQ=255)
                                                                           ttAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGa                                                                                      >  2:184111/1‑72 (MQ=255)
                                                                            tAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTATAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTTGTGCGATCAGGCATTCTCGAATTAATGGTGATGgt         <  4:469674/148‑1 (MQ=255)
                                                                               tctcTTCAACCTTGTCAAGGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGc                                               <  3:705625/107‑1 (MQ=255)
                                                                               tctcTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGc                                               >  4:705625/1‑107 (MQ=255)
                                                                                ctctTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTTGTGCGATCAGGCATtct                           <  4:339510/126‑1 (MQ=255)
                                                                                ctctTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTTGTGCGATCAGGCATtct                           >  3:339510/1‑126 (MQ=255)
                                                                                    tCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATaaa                                                                                          >  2:135766/1‑59 (MQ=255)
                                                                                    tCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATaaa                                                                                          <  1:135766/59‑1 (MQ=255)
                                                                                    tCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTTGTGCGATCAGGCATTCTCGAATTAATGGTGATGGTCGTCAAt  >  1:216627/1‑147 (MQ=255)
                                                                                    tCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTTGTGCGATCAGGCATTCTCGAATTAATGGTGATGGTCGTCAAt  <  2:216627/147‑1 (MQ=255)
                                                                                                aCGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATg                                                        >  3:560239/1‑81 (MQ=255)
                                                                                                aCGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATg                                                        <  4:560239/81‑1 (MQ=255)
                                                                                                 cGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTTGTGCGATCAGGCATTCTCGAATTaa                   >  4:840847/1‑117 (MQ=255)
                                                                                                 cGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTTGTGCGATCAGGCATTCTCGAATTaa                   <  3:840847/117‑1 (MQ=255)
                                                                                                   gAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATa                                                                                            >  1:193139/1‑42 (MQ=255)
                                                                                                   gAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATa                                                                                            <  2:193139/42‑1 (MQ=255)
                                                                                                            ggCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTtg                                           <  4:699485/82‑1 (MQ=255)
                                                                                                            ggCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTtg                                           >  3:699485/1‑82 (MQ=255)
                                                                                                                     tGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTTGTGCGATCAGGCATTCTCGAATTAATGGTGATGgt         <  1:274303/107‑1 (MQ=255)
                                                                                                                     tGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTTGTGCGATCAGGCATTCTCGAATTAATGGTGATGgt         >  2:274303/1‑107 (MQ=255)
                                                                                                                      gATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTTGTGCGATCAGGCATTCTCGAATTa                    <  1:761573/95‑1 (MQ=255)
                                                                                                                      gATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTTGTGCGATCAGGCATTCTCGAATTa                    >  2:761573/1‑95 (MQ=255)
                                                                                                                              tCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAg                                                                    <  1:149223/39‑1 (MQ=255)
                                                                                                                              tCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAg                                                                    >  2:149223/1‑39 (MQ=255)
                                                                                                                                    |                                                                                                  
TGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTGGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAAAAAAATGCCTGACTGCTTTGTGCGATCAGGCATTCTCGAATTAATGGTGATGGTCGTCAAT  >  NC_000913/884736‑884966

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A