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 104 44.1 1376607 98.9% 1361464 150.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,634,685 G→A intergenic (‑227/‑156) yhiL ← / → yhiM pseudogene, DUF4049 family protein/acid resistance protein, inner membrane

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,634,6850GA97.9% 177.1 / ‑4.1 47intergenic (‑227/‑156)yhiL/yhiMpseudogene, DUF4049 family protein/acid resistance protein, inner membrane
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (25/21);  total (26/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

AATAATAATACTTATATGTTCGCTGATTTTAAGCACCGAGACTATCCGGTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGGCCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGAAATTATCATTAATGCATATTTCAATATTAGCA  >  NC_000913/3634538‑3634819
                                                                                                                                                   |                                                                                                                                      
aataataatACTTATATGTTCGCTGATTTTAAGCACCGAGACTATCCGGTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCt                                                                                                                                     >  2:90088/1‑151 (MQ=255)
 ataataataCTTATATGTTCGCTGATTTTAAGCACCGAGACTATCCGGTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCtt                                                                                                                                    >  1:342336/1‑151 (MQ=255)
     taataGTTATATGTTCGCTGATTTTAAGCACCGAGACTATCCGGGCTTTTACCAAAGAATGAAGAATAATCCATCCATGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTg                                                                                                                                 >  1:421567/1‑150 (MQ=255)
     taataCTTATATGTTCGCTGATTTTAAGCACCGAGACTATCCGGTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGGCCTTTTg                                                                                                                                 >  2:445414/1‑150 (MQ=255)
           ttATATGTTCGCTGATTTTAAGCACCGAGACTATCCGGTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTg                                                                                                                          >  2:292424/1‑151 (MQ=255)
            tataTGTTCGCTGATTTTAAGCACCGAGACTATCCGGTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTg                                                                                                                          >  2:50024/1‑150 (MQ=255)
                  ttCGCTGATTTTAAGCACCGAGACTATCCGGTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGt                                                                                                                    >  1:513642/1‑150 (MQ=255)
                    cGCTGATTTTAAGCACCGAGACTATCCGGTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAgc                                                                                                                 >  2:193195/1‑151 (MQ=255)
                          ttttAAGCACCGAGACTATCCGGTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTg                                                                                                           >  1:246711/1‑151 (MQ=255)
                                           aTCCGGTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCta                                                                                          <  1:648027/151‑1 (MQ=255)
                                           aTCCGGTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCta                                                                                          <  1:554843/151‑1 (MQ=255)
                                             ccGGTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCtat                                                                                         >  2:290642/1‑150 (MQ=255)
                                              cGGTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAg                                                                                       <  2:69008/151‑1 (MQ=255)
                                                gTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGtt                                                                                     <  1:84869/151‑1 (MQ=255)
                                                    tttACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTtatgc                                                                                 >  1:72708/1‑151 (MQ=255)
                                                    tttACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTtat                                                                                   <  1:109602/149‑1 (MQ=255)
                                                     ttACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTtatgct                                                                                >  1:521483/1‑151 (MQ=255)
                                                        ccAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTtatgctatg                                                                             >  2:190416/1‑151 (MQ=255)
                                                           aataatGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCAt                                                                          <  2:492834/151‑1 (MQ=255)
                                                                 gaagaaTAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATAATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCt                                                                    >  1:419009/1‑151 (MQ=255)
                                                                  aagaaTAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGGTAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCtt                                                                   >  2:671326/1‑151 (MQ=255)
                                                                           ccctccctGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGata                                                           <  1:63826/150‑1 (MQ=255)
                                                                            cctccctGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATAtc                                                         <  2:170335/151‑1 (MQ=255)
                                                                                     aaGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCAtt                                                 >  1:141172/1‑150 (MQ=255)
                                                                                        aTAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTatat                                             <  1:386071/151‑1 (MQ=255)
                                                                                        aTAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTatat                                             <  1:220225/151‑1 (MQ=255)
                                                                                          aaTTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATAtt                                            >  1:7184/1‑150 (MQ=255)
                                                                                                 aaaaaCAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGAt                                    <  1:190413/151‑1 (MQ=255)
                                                                                                  aaaaCAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATg                                   >  1:422002/1‑151 (MQ=255)
                                                                                                  aaaaCAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATg                                   >  2:430689/1‑151 (MQ=255)
                                                                                                    aacaacAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGaa                                 <  1:150901/151‑1 (MQ=255)
                                                                                                     acaacaGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGaaa                                <  1:118208/151‑1 (MQ=255)
                                                                                                            cATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGAAATTATCAt                         >  2:96894/1‑151 (MQ=255)
                                                                                                             aTAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATg                                   >  2:529049/1‑140 (MQ=255)
                                                                                                             aTAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATg                                   <  1:529023/140‑1 (MQ=255)
                                                                                                             aTAAGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGAAATTATCAtt                        <  2:515872/151‑1 (MQ=255)
                                                                                                               aaGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCTTCATTATATTAACAGGATGAAATTATCATTa                       <  2:487509/150‑1 (MQ=255)
                                                                                                               aaGAATTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGAAATTATCATTa                       <  2:270235/150‑1 (MQ=255)
                                                                                                                  aaTTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGAAATTATCATTAATGc                   >  1:310424/1‑151 (MQ=255)
                                                                                                                  aaTTAATCTTAGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGAAATTATCATTAATGc                   >  2:160571/1‑151 (MQ=255)
                                                                                                                            aGGATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGAAATTATCATTAATGCATATTTCaa          <  2:811/150‑1 (MQ=255)
                                                                                                                             ggATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGAAATTATCATTAATGCATATTTCAata        <  1:616259/151‑1 (MQ=255)
                                                                                                                              gATAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGAAATTATCATTAATGCATATTTCAatat       >  2:416052/1‑151 (MQ=255)
                                                                                                                                tAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGAAATTATCATTAATGCATATTTCAATAtt      >  2:541761/1‑150 (MQ=255)
                                                                                                                                tAAATTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGAAATTATCATTAATGCATATTTCAATAtt      >  1:10150/1‑150 (MQ=255)
                                                                                                                                   aTTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGAAATTATCATTAATGCATATTTCAATATTAGCa  <  2:419022/151‑1 (MQ=255)
                                                                                                                                   aTTTTTATTTATCATGACCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGAAATTATCATTAATGCATATTTCAATATTAGCa  <  1:324125/151‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                      
AATAATAATACTTATATGTTCGCTGATTTTAAGCACCGAGACTATCCGGTCTTTTACCAAATAATGAAGAATAATCCCTCCCTGGAAGATAATTGTAAAAAACAACAGCATAAGAATTAATCTTAGGATAAATTTTTATTTATCATGGCCTTTTGAACGCTGAAAAGTAGCGCTCTGCAAAGTAAACCCCGCTATAGTTATGCTATGCATTTGTCTTTAATGATATCTCGTCATTATATTAACAGGATGAAATTATCATTAATGCATATTTCAATATTAGCA  >  NC_000913/3634538‑3634819

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A