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
A4 F50 I2 R1 11 44.6 1622634 97.7% 1585313 150.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,230,727 C→A intergenic (‑333/‑40) hlyE ← / → umuD hemolysin E/translesion error‑prone DNA polymerase V subunit; RecA‑activated auto‑protease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,230,7270CA98.0% 192.9 / NA 51intergenic (‑333/‑40)hlyE/umuDhemolysin E/translesion error‑prone DNA polymerase V subunit; RecA‑activated auto‑protease
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (22/28);  total (23/28)
Fisher's exact test for biased strand distribution p-value = 4.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGGTGATATTTTTCATTTCTGCTGGATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGACTACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCTTTCCTTCACCGGCAGCAGATTACGTTGA  >  NC_000913/1230584‑1230870
                                                                                                                                               |                                                                                                                                               
gggTGATATTTTTCATTTCTGCTGGATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGt                                                                                                                                           >  2:577553/1‑150 (MQ=255)
gggTGATATTTTTCATTTCTGCTGGATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGt                                                                                                                                           >  1:512973/1‑150 (MQ=255)
    gATATTTTTCATTTCTGCTGGATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGtatata                                                                                                                                      <  1:25376/151‑1 (MQ=255)
     atatTTTTCATTTCTGCTGGATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGtatata                                                                                                                                      >  1:323763/1‑150 (MQ=255)
      tatTTTTCATTTCTGCTGTATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGATAACTAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACATAATACTGtatata                                                                                                                                      <  1:25393/149‑1 (MQ=255)
      tatTTTTCATTTCTGCTGGATGAGCGTCGTCGCCAGAAGGCCACGTGATCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATaa                                                                                                                                     >  1:153380/1‑150 (MQ=255)
      tatTTTTCATTTCTGCTGGATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATaa                                                                                                                                     >  2:102553/1‑150 (MQ=255)
       atTTTTCATTTCTGCTGGATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATaaa                                                                                                                                    <  2:261440/150‑1 (MQ=255)
           ttCATTTCTGCTGGATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACa                                                                                                                                <  2:100540/150‑1 (MQ=255)
             cATTTCTGCTGGATGAGCGTCGTCGCCATAAGGCCACGTGAGCACGAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTTATAGCATGAATCAGTATTGATCTGCTGGCAAGAACAGAATCCTGTATATAAAAACAGta                                                                                                                             <  1:73633/151‑1 (MQ=255)
             cATTTCTGCTGGATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGta                                                                                                                             <  1:776982/151‑1 (MQ=255)
                ttCTGCTGGATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGtata                                                                                                                           <  1:658851/150‑1 (MQ=255)
                 tCTGCTGGATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATaa                                                                                                                          <  2:701548/150‑1 (MQ=255)
                    gctgGATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAAc                                                                                                                         <  2:499803/148‑1 (MQ=255)
                        gATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAgg                                                                                                                   <  1:164811/150‑1 (MQ=255)
                         aTGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGc                                                                                                                  >  2:538779/1‑150 (MQ=255)
                             gCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGatt                                                                                                             <  1:535705/151‑1 (MQ=255)
                                 cgtcgCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGattatt                                                                                                          >  2:322217/1‑150 (MQ=255)
                                 cgtccCCAGACGGCAACGTGAGCACAAGATAAGAGAACAAAAAATCAGCAGCCAATGCAGCGACAAATATTGATAGCATGAATCAGAATTGATCTGCTAGCAAGCACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGattatt                                                                                                          >  1:701745/1‑150 (MQ=255)
                                            ggCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATc                                                                                              <  2:353245/151‑1 (MQ=255)
                                             gCCCCGTGTGCACACGTTCAGAGCACGAAAAATTAGCAGCCTATGAGGAGACAAATATTGACAGCCTGAATCAGTATTGAACTGCTGGCAAGAACAGACTACTGTATATAACAAACGTATAACTTCAGGCAAATTCTTCTGTTGTTTAt                                                                                               >  1:789319/1‑149 (MQ=255)
                                              ccACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCaa                                                                                            <  2:38196/151‑1 (MQ=255)
                                                  gTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCt                                                                                        <  1:225589/151‑1 (MQ=255)
                                                    gAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTg                                                                                       <  2:655073/150‑1 (MQ=255)
                                                        acaAGATAAGAGAACGAAAAATCGGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGa                                                                                   <  1:718390/150‑1 (MQ=255)
                                                             aTAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCcg                                                                             >  1:86753/1‑151 (MQ=255)
                                                                  agaACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGaa                                                                         >  2:632993/1‑150 (MQ=255)
                                                                     aCGACAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAAt                                                                       >  1:523992/1‑149 (MQ=255)
                                                                               agcagcCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTcc                                                           <  1:792407/151‑1 (MQ=255)
                                                                                 cagcCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGc                                                         <  2:39265/151‑1 (MQ=255)
                                                                                       aTGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTAttt                                                    <  1:681197/150‑1 (MQ=255)
                                                                                       aTGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTAttt                                                    <  2:226926/150‑1 (MQ=255)
                                                                                       aTGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTa                                                   <  2:759615/151‑1 (MQ=255)
                                                                                               aCAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCtt                                           <  2:414633/151‑1 (MQ=255)
                                                                                                 aaaTATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGt                                         >  1:727251/1‑151 (MQ=255)
                                                                                                 aaaTATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGt                                         >  1:589272/1‑151 (MQ=255)
                                                                                                   atatTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTc                                       >  2:202592/1‑151 (MQ=255)
                                                                                                     atTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAg                                     <  2:135310/151‑1 (MQ=255)
                                                                                                             ccTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCtt                             <  2:139727/151‑1 (MQ=255)
                                                                                                              cTGAATCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCttt                            >  1:329923/1‑151 (MQ=255)
                                                                                                                  aTCAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCTTTCCtt                        >  1:217101/1‑151 (MQ=255)
                                                                                                                    cAGTATTGATCTGCTGGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCTTTCCTTc                       <  1:373781/150‑1 (MQ=255)
                                                                                                                              ctgctgGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCTTTCCTTCACCGgcagc              >  1:596739/1‑149 (MQ=255)
                                                                                                                               tgctgGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCTTTCCTTCACCGgcagc              >  1:312368/1‑148 (MQ=255)
                                                                                                                               tgctgGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCTTTCCTTCACCGgcagc              >  2:768056/1‑148 (MQ=255)
                                                                                                                                gctgGCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCTTTCCTTCACCGGcagcag            <  1:322178/149‑1 (MQ=255)
                                                                                                                                   ggCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCTTTCCTTCACCGGCAGCAGATTAc       <  1:612010/151‑1 (MQ=255)
                                                                                                                                    gCAAGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCATGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCTTTCCTTCACCGGCAGCAGATTACg      >  1:254720/1‑151 (MQ=255)
                                                                                                                                       aGAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCTTTCCTTCACCGGCAGCAGATTACGtt    >  2:336319/1‑150 (MQ=255)
                                                                                                                                        gAACAGAATACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCTTTCCTTCACCGGCAGCAGATTACGTTGa  <  1:770918/151‑1 (MQ=255)
                                                                                                                                         aaCAGAATACTGTATATAAAAACAGTATAACTTCCGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCTTTCCTTCACCGGCAGCAGATTACGtt    >  1:781875/1‑148 (MQ=255)
                                                                                                                                               |                                                                                                                                               
GGGTGATATTTTTCATTTCTGCTGGATGAGCGTCGTCGCCAGAAGGCCACGTGAGCACAAGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCGACAAATATTGATAGCCTGAATCAGTATTGATCTGCTGGCAAGAACAGACTACTGTATATAAAAACAGTATAACTTCAGGCAGATTATTATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGTGTGGCTTTCCTTCACCGGCAGCAGATTACGTTGA  >  NC_000913/1230584‑1230870

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A