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
A9 F28 I1 R1 120 56.0 1898522 99.4% 1887130 138.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,286,746 G→A L159L (CTG→CTA)  agaI → putative deaminase AgaI

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,286,7460GA95.7% 146.7 / ‑1.5 46L159L (CTG→CTA) agaIputative deaminase AgaI
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base A (17/27);  total (18/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.81e-01

TGAAGACCAGCTCATCAGCTTTCGCTCCGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGTCGCCCCGTGACTCGTGGGATCACCTTAGGCCTGAAGGATA  >  NC_000913/3286611‑3286876
                                                                                                                                       |                                                                                                                                  
tGAAGACCAGCTCATCAGCTTTCGCTCCGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTaaacg                                                                                                                                >  2:298210/1‑140 (MQ=255)
  aaGACCAGCTCATCAGCTTTCGCTCCGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTaaacgaa                                                                                                                              <  2:20921/140‑1 (MQ=255)
  aaGACCAGCTCATCAGCTTTCGCTCCGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTaaacgaa                                                                                                                              <  1:795640/140‑1 (MQ=255)
    gACCAGCTCATCAGCTTTCGCTCCGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAAcc                                                                                                                            <  2:891664/140‑1 (MQ=255)
    gACCAGCTCATCAGCTTTCGCTCCGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAAcc                                                                                                                            >  2:230245/1‑140 (MQ=255)
        aGCTCATCAGCTTTCGCTCCGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGga                                                                                                                        >  1:383495/1‑140 (MQ=255)
          cTCATCAGCTTTCGCTCCGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGgaga                                                                                                                      <  1:134011/140‑1 (MQ=255)
             atcaGCTTTCGCTCCGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAg                                                                                                                   >  1:812860/1‑140 (MQ=255)
                    ttCGCTCCGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCaa                                                                                                            <  1:349153/140‑1 (MQ=255)
                    ttCGCTCCGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCaa                                                                                                            <  1:675600/140‑1 (MQ=255)
                       gCTCCGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCg                                                                                                         <  1:298210/140‑1 (MQ=255)
                          ccGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGcc                                                                                                      <  2:812860/140‑1 (MQ=255)
                            gAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATAGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCGGGAGAAAGCCTGCAACCgg                                                                                                        >  1:441425/1‑136 (MQ=255)
                            gAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATAGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCGGGAGAAAGCCTGCAACCgg                                                                                                        <  2:441425/136‑1 (MQ=255)
                                           aCAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACt                                                                                     >  2:255646/1‑140 (MQ=255)
                                               agTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCa                                                                                                 <  2:5022/124‑1 (MQ=255)
                                               agTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCa                                                                                                 >  1:5022/1‑124 (MQ=255)
                                               agTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGAt                                                                                 >  2:728492/1‑140 (MQ=255)
                                                 tGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGGTTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGc                                                                               <  1:303787/140‑1 (MQ=255)
                                                    gAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAg                                                                            <  1:948451/140‑1 (MQ=255)
                                                      aCGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGaa                                                                          >  1:580281/1‑140 (MQ=255)
                                                         ggTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGCTTGATGTGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAAAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAacac                                                                       <  2:81691/140‑1 (MQ=255)
                                                         ggTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAg                                                                            <  1:824279/135‑1 (MQ=255)
                                                         ggTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAg                                                                            >  2:824279/1‑135 (MQ=255)
                                                         ggTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAacac                                                                       >  1:115365/1‑140 (MQ=255)
                                                             aCGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCa                                                                   >  1:273226/1‑140 (MQ=255)
                                                                  ccTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGGCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATg                                                              >  2:479923/1‑140 (MQ=255)
                                                                  ccTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATg                                                              >  2:347959/1‑140 (MQ=255)
                                                                  ccTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATg                                                              >  2:40659/1‑140 (MQ=255)
                                                                    tGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATgag                                                            <  1:728492/140‑1 (MQ=255)
                                                                    tGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATgag                                                            >  2:909528/1‑140 (MQ=255)
                                                                         gcgcgcAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGtt                                                       >  2:522415/1‑140 (MQ=255)
                                                                             gcAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTaaaa                                                   >  2:352192/1‑140 (MQ=255)
                                                                                aaGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAAcc                                                <  1:255646/140‑1 (MQ=255)
                                                                                     ggTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCggg                                           <  2:383495/140‑1 (MQ=255)
                                                                                     ggTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGATAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCggg                                           <  2:768199/140‑1 (MQ=255)
                                                                                      gTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGt                                          <  1:347959/140‑1 (MQ=255)
                                                                                      gTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGt                                          <  2:702347/140‑1 (MQ=255)
                                                                                       tCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGTc                                         >  2:69183/1‑140 (MQ=255)
                                                                                             tttATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGGCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGTCGCCCCg                                   <  1:479923/140‑1 (MQ=255)
                                                                                              ttATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGTCGCCCCGt                                  <  2:278939/140‑1 (MQ=255)
                                                                                              ttATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGTCGCCCCGt                                  <  1:937247/140‑1 (MQ=255)
                                                                                              ttATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGTCGCCCCGt                                  <  1:40659/140‑1 (MQ=255)
                                                                                                     ttCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGTCGCCCCGTGACTCGt                           <  2:938319/140‑1 (MQ=255)
                                                                                                     ttCTCGGATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGTCGCCCCGTGACTCGt                           <  2:273226/140‑1 (MQ=255)
                                                                                                          ggATTGGGGAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGTCGCCCCGTGACTCGTGGGAt                      <  2:580281/140‑1 (MQ=255)
                                                                                                               ggggAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGTCGCCCCGTGACTCGTGGGATCACCt                 <  1:909528/140‑1 (MQ=255)
                                                                                                                 ggAAAAACGGTCATCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGTCGCCCCGTGACTCGTGGGATCACCTTa               <  1:522415/140‑1 (MQ=255)
                                                                                                                              tCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGTCGCCCCGTGACTCGTGGGATCACCTTAGGCCTGAAGGata  <  1:60846/140‑1 (MQ=255)
                                                                                                                              tCTTGGGCTAAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGTCGCCCCGTGACTCGTGGGATCACCTTAGGCCTGAAGGata  <  1:339969/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                  
TGAAGACCAGCTCATCAGCTTTCGCTCCGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCGGGAGAAAGCCTGCAACCGGCCTGCCATATCAGTCAACTTGATGCCAGAACACAGCAACATGAGATGTTAAAAACCGCGGGTCGCCCCGTGACTCGTGGGATCACCTTAGGCCTGAAGGATA  >  NC_000913/3286611‑3286876

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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