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
A21 F97 I0 R1 51 42.6 1617048 90.7% 1466662 142.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 595,519 T→A 7.9% intergenic (‑76/‑81) cusR ← / → cusC DNA‑binding transcriptional activator CusR/copper/silver export system outer membrane channel

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913595,5190TA 7.9% 127.0 / 2.5 47intergenic (‑76/‑81)cusR/cusCDNA‑binding transcriptional activator CusR/copper/silver export system outer membrane channel
Reads supporting (aligned to +/- strand):  ref base T (19/24);  new base A (2/2);  total (21/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.68e-01

GTTAACCCTTTGGTCAAGTATTCTCCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTGCGCTAACCGGTTGTTCACT  >  NC_000913/595382‑595658
                                                                                                                                         |                                                                                                                                           
gTTAACCCTTTGGTCAAGTATTCTGCGGTTTTCTTTTCATCTTGGACAATCAACAGTTTCATATTTGCTCCGCATGTTGCCCGGGCAAATCTAGAGTAGCGGGATCCCATGGCAATGTCTTATTGGAAAAAGGAACATTTTGt                                                                                                                                        >  2:456526/1‑143 (MQ=255)
      ccTTTGGTCAAGTATTCTCCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAAAATTGTCAtttt                                                                                                                                  <  2:392183/143‑1 (MQ=255)
        tttGTTCAATTATTCTCCGGTTTTCTTTACAACGACGACAAGCAACAGGCTCATATTGCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAAAATTGTCAttttgc                                                                                                                                <  1:5884/143‑3 (MQ=255)
           ggTCAAGTATTCTCCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGt                                                                                                                             <  1:61528/143‑1 (MQ=255)
                aGTATTCTCCGGTTTTCTTTTCATCTTCGACAAGCAACGGGTTCATATTTCCTCCGCATGTTGCCCGGGCACTTCTAGAGTAGCGGGATCAGATTGCACTCGCTTATTCGTAAAGTTACAAATTTGTCCTTTTTCTGCCAGCg                                                                                                                        >  2:704181/1‑143 (MQ=255)
                   actctcCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGaa                                                                                                                     <  1:537246/141‑1 (MQ=255)
                    ttCCCCGGTTCTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCGCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGaaa                                                                                                                    <  2:456796/143‑1 (MQ=255)
                     tctcCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACACTTTTGTCATTTTTCTGTCACCGGgaaa                                                                                                                   >  1:104728/1‑143 (MQ=255)
                     tctcCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCCCATGTTGCCCGTGCCATTCTCGAGTAGCGTGATCAGATGGCAATCGCTTCTTGGCAAACTCCCAATTCTGTCATCTTTCTTTCACCGGacaa                                                                                                                   >  2:376819/1‑143 (MQ=255)
                       tcCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATc                                                                                                                 >  2:186503/1‑143 (MQ=255)
                        ccGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCa                                                                                                                <  1:120627/143‑1 (MQ=255)
                          gttcttcttttcATCTTCTACAAGCAACAGTTTCATATTTCCTCCGCATGTTGCCCTGGCAATTCTAGAGTAGCGGGTTCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCaga                                                                                                              <  2:83543/139‑1 (MQ=255)
                              ttcttttcATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCt                                                                                                          >  1:446816/1‑143 (MQ=255)
                                 ttttcATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCCGATGGCAATCGCTCATTGGCAAAATGACAATTTTGTCCTTTTTATGTCGCCGGAGACTCAGAGccacgc                                                                                                       >  2:731169/1‑139 (MQ=255)
                                   ttcATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGa                                                                                                     <  1:186503/143‑1 (MQ=255)
                                      aTCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAAGCAGGGCATGGCGAGTa                                                                                                  >  2:674174/1‑143 (MQ=255)
                                       tCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTaa                                                                                                 >  2:453830/1‑143 (MQ=255)
                                        cTTCGAGAATCACCGGTTTAATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTaaa                                                                                                <  2:729667/143‑1 (MQ=255)
                                         ttCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAg                                                                                               >  1:264773/1‑143 (MQ=255)
                                          tCGACCATCAACCGTTTCATATTGCCTCCGCATGTTGCCCGGGCAAGTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGt                                                                                              <  2:636960/143‑1 (MQ=255)
                                                  cAACGGCTTCACATTTCCTCCGCATCTTGCCCGGGCAATGCGAGATTAGCGGGAGCAGATTGCAACCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCa                                                                                      <  2:11812/143‑1 (MQ=255)
                                                        tttCATATTCCCTCCGCCTGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAAt                                                                                <  1:293174/143‑1 (MQ=255)
                                                         tccacacttCCTGCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATc                                                                               <  1:291616/136‑1 (MQ=255)
                                                          tCATATTTCCTCCGCTTGTGGACCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCa                                                                              <  2:485226/143‑1 (MQ=255)
                                                                 tcctccGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGaaa                                                                       >  2:147290/1‑143 (MQ=255)
                                                                  cctccGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGGAAATCAGAGCCTGGCGAGTAAAGTTGGAGGCGTAAGATCACCAGaagt                                                                      >  1:152089/1‑141 (MQ=255)
                                                                  cctccGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGCGTACTGTTGGCGGCATAAAATCACCAGAAAt                                                                      >  1:443007/1‑143 (MQ=255)
                                                                    tcggCATGTTGCCCGGGCAGTTCTAGAGTGGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAAGCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTa                                                                    <  2:555924/140‑1 (MQ=255)
                                                                      cGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATGACCAGAAATTATg                                                                  >  2:389020/1‑143 (MQ=255)
                                                                         aTGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGc                                                               <  1:529787/143‑1 (MQ=255)
                                                                                 cgggacaTTCTTGAGTGGTGGGATCGTATGGCAATCCCTTATTGGCAAAATCACAATGTTGGCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGtct                                                       <  2:527349/137‑1 (MQ=255)
                                                                                 cGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTGTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTACGAGCCTATGtca                                                       >  2:30507/1‑142 (MQ=255)
                                                                                   ggCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTcc                                                     <  2:519647/143‑1 (MQ=255)
                                                                                     cAATTCTAGAGAAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCtt                                                   <  1:551452/143‑1 (MQ=255)
                                                                                      aaTTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACGATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGGGCCTATGTCACCtgg                                                  >  2:137844/1‑141 (MQ=255)
                                                                                             gagTAGCGTGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACtt                                           <  2:585154/143‑1 (MQ=255)
                                                                                                  gCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGcc                                      >  2:657109/1‑143 (MQ=255)
                                                                                                     ggATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCAtt                                   <  1:671519/143‑1 (MQ=255)
                                                                                                            acggCAATCGCTTATTGGCAAAATAACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTtgtgtg                            <  2:229460/141‑1 (MQ=255)
                                                                                                             gggCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTGCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTgg                           <  2:147788/142‑1 (MQ=255)
                                                                                                                    cggttATTGGCAAAATGACAATTTTGTCATTGTTCTGTCAGCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCGGCCATTTTGTGTGGCCCTTgc                    <  2:718382/140‑1 (MQ=255)
                                                                                                                    cGCTGATTGGCAAAATGACAATTTTGTCATGTGTCTGTCGCCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTgc                    <  2:366861/143‑1 (MQ=255)
                                                                                                                      cTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTgcgc                  >  1:801987/1‑143 (MQ=255)
                                                                                                                            agaaaaaTGACAAAATTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTGCGCTAACCg            >  2:173328/4‑143 (MQ=255)
                                                                                                                               aaaaTGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTGCGCTAACCGgtt         <  1:363571/143‑1 (MQ=255)
                                                                                                                                      cAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTGCGCTAACCGGTTGTTCACt  >  1:282808/1‑143 (MQ=255)
                                                                                                                                      cAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTGCGCTAACCGGTTGTTCACt  >  1:296974/1‑143 (MQ=255)
                                                                                                                                         |                                                                                                                                           
GTTAACCCTTTGGTCAAGTATTCTCCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTGCGCTAACCGGTTGTTCACT  >  NC_000913/595382‑595658

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A