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
A19 F106 I1 R1 27 57.4 1363720 95.8% 1306443 135.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,010,363 C→T C146Y (TGT→TAT)  USA300HOU_RS10125 ← Putative multidrug export ATP‑binding/permease protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,010,3630CT97.7% 133.3 / ‑5.5 44C146Y (TGT→TAT) USA300HOU_RS10125Putative multidrug export ATP‑binding/permease protein
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (14/29);  total (14/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

GTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGG  >  USA300TCH1516_ALE/2010234‑2010494
                                                                                                                                 |                                                                                                                                   
gtCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCATATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCt                                                                                                                                <  1:85904/135‑1 (MQ=255)
    aatttCTTTATCCTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATACACCGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATAGATTGTGCCATAATAATTGTTATATAATCTAAcc                                                                                                                            <  2:503720/133‑1 (MQ=255)
    aTTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCATATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAAcc                                                                                                                            <  1:205572/135‑1 (MQ=255)
    aTTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAAATACACAAATAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAAcc                                                                                                                            <  2:285883/135‑1 (MQ=255)
          ttAATCTTCCAAAGATAATATACACCATTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAatat                                                                                                                      >  1:670152/1‑135 (MQ=255)
                ttCCAAAGAAACCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTa                                                                                                                <  1:584249/135‑1 (MQ=255)
                ttCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGTAATAATAATTGTTATATAATCTAACCAAATATTCATTa                                                                                                                <  1:611909/135‑1 (MQ=255)
                 tCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATTTAACCAAATATTCATTaa                                                                                                               >  2:609992/1‑135 (MQ=255)
                      aGAAAACGTACACCGTTAAAATGTCAATTGGGAAGATAAACAGGCCCGCTCAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCgg                                                                                                          <  2:72937/135‑1 (MQ=255)
                       gAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGt                                                                                                         >  1:163002/1‑135 (MQ=255)
                        aaaaCGTACACCGTTAAAATGTAAAATTGGAAGATAAACAGGGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATCATCTAACCAAATATTCATTAACCCGGtt                                                                                                        <  2:634734/135‑1 (MQ=255)
                                   cGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATc                                                                                             <  1:55807/135‑1 (MQ=255)
                                     ttAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCtt                                                                                           <  1:483447/135‑1 (MQ=255)
                                      taaaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCgtt                                                                                          <  1:27190/135‑1 (MQ=255)
                                          atgtaaaatgGGAAGATAAACAGTGCTGCTAATGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAATCAAATATTCATTAACCCGGTTAATATGAAATCTtttgtt                                                                                      <  2:305396/135‑1 (MQ=255)
                                          atgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTTTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttgtt                                                                                      <  1:675732/135‑1 (MQ=255)
                                          atgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttgtt                                                                                      >  1:379010/1‑135 (MQ=255)
                                          atgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttgtt                                                                                      <  1:675752/135‑1 (MQ=255)
                                          atgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttgtt                                                                                      <  2:111539/135‑1 (MQ=255)
                                          atgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttgtt                                                                                      <  2:134003/135‑1 (MQ=255)
                                                   gggAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAca                                                                             <  2:316496/135‑1 (MQ=255)
                                                      aaGAAAAACAGTGCTGCTAAAATCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatca                                                                          >  1:458867/1‑135 (MQ=255)
                                                          tAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTaa                                                                      >  2:93025/1‑135 (MQ=255)
                                                             aCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCa                                                                   >  2:348724/1‑135 (MQ=255)
                                                             aCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAATGCAATAATAATTGTTATATAACCTAACCAAATATTCATTAACCTTGTTAAAATGAAATTTTTTGTTTGTTCAACATCATTAATCa                                                                   <  1:165742/135‑1 (MQ=255)
                                                                         aaGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGTAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTa                                                       <  2:379010/135‑1 (MQ=255)
                                                                               aTTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGAc                                                 >  2:57128/1‑135 (MQ=255)
                                                                                    acaTCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTGCt                                            >  2:428480/1‑135 (MQ=255)
                                                                                        cTAAAAAGAACATTATGGCTAGTACAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACACTAAATATTAATTGACCTACTTGat                                        >  2:254602/1‑135 (MQ=255)
                                                                                         tAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGatt                                       >  2:290711/1‑135 (MQ=255)
                                                                                          aaaaaGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATTACATCTTTTGTTTGTTCAACATCTTTATTCACTCTAGATATTACTTTTCCTACTTGatta                                      <  2:624361/135‑1 (MQ=255)
                                                                                          aaaaaGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCTCTCTAGATATTACTTGACCTACTTGatta                                      <  1:179993/135‑1 (MQ=255)
                                                                                          aaaaaGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGatta                                      <  2:262812/135‑1 (MQ=255)
                                                                                                aaCATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTCGATATTACTTGACCTACTTGATTATTAGCa                                <  2:360243/135‑1 (MQ=255)
                                                                                                       tGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAAtc                         >  1:310111/1‑135 (MQ=255)
                                                                                                          aTAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCg                      <  2:39787/135‑1 (MQ=255)
                                                                                                          aTAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCg                      <  2:359548/135‑1 (MQ=255)
                                                                                                                cAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGTATAAAATCTCGCACTTa                <  1:534251/135‑1 (MQ=255)
                                                                                                                  ataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTaac              >  2:277777/1‑134 (MQ=255)
                                                                                                                  ataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTaaa              <  1:428480/135‑1 (MQ=255)
                                                                                                                        atTTTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGt        <  2:257790/135‑1 (MQ=255)
                                                                                                                        atTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGt        <  2:64614/135‑1 (MQ=255)
                                                                                                                        atTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGt        <  2:20756/135‑1 (MQ=255)
                                                                                                                            ttATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGATTGTAAAt    >  1:233787/1‑135 (MQ=255)
                                                                                                                              atatAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATgg  <  1:57128/135‑1 (MQ=255)
                                                                                                                                 |                                                                                                                                   
GTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGG  >  USA300TCH1516_ALE/2010234‑2010494

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A