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
A1 F15 I0 R1 22 59.5 1335882 95.9% 1281110 140.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,010,363 C→T 100% 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_ALE2,010,3630CT100.0% 165.2 / NA 54C146Y (TGT→TAT) USA300HOU_RS10125Putative multidrug export ATP‑binding/permease protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (28/26);  total (28/26)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGG  >  USA300TCH1516_ALE/2010234‑2010494
                                                                                                                                 |                                                                                                                                    
gtCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTTAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCa                                                                                                                            <  1:175099/140‑1 (MQ=255)
 tCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAGAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCaa                                                                                                                           >  1:576860/1‑140 (MQ=255)
  cAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCaaa                                                                                                                          >  2:296089/1‑140 (MQ=255)
  cAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCaaa                                                                                                                          >  2:494527/1‑140 (MQ=255)
   aaTTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAat                                                                                                                         >  1:632926/1‑140 (MQ=255)
        tCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCACTTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAAAATTCa                                                                                                                    >  1:425265/1‑140 (MQ=255)
            aaTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑Taa                                                                                                               >  1:406321/1‑140 (MQ=255)
             aTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGAGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAAc                                                                                                              >  1:622621/1‑140 (MQ=255)
              tgttCCAAAGTAAACGTACACCGTGAAAATGTAAAATGGGGATATCATCAGTGCTGCTAAATCCAATTTCACAGCTAAAAAGAACTTTCTGGACAGTGCAATAATGATTGTTATTTAATCTAACCAAATATTCAT‑TAAcc                                                                                                             <  2:154392/138‑1 (MQ=255)
               cTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTAAATAATATAACCAAATAATTAT‑TAAccc                                                                                                            >  2:100778/1‑140 (MQ=255)
                 tCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCACTCATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCgg                                                                                                          <  2:607734/140‑1 (MQ=255)
                   cAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGtt                                                                                                        <  2:522419/140‑1 (MQ=255)
                         acccggacacCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATg                                                                                                  <  2:633897/134‑1 (MQ=255)
                         aatcGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATg                                                                                                  <  2:170387/137‑1 (MQ=255)
                         aaaCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATCATT‑TAACCCGGTTaaaaag                                                                                                  >  2:77573/1‑138 (MQ=255)
                           aCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGaa                                                                                                >  1:18044/1‑140 (MQ=255)
                             gTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAAt                                                                                              <  1:607662/140‑1 (MQ=255)
                               acacCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCt                                                                                            <  2:456591/140‑1 (MQ=255)
                                    gTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTtttgt                                                                                       >  2:550425/1‑140 (MQ=255)
                                          atgtaaaatgGCAAGATAACCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATCATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTc                                                                                 <  2:155150/140‑1 (MQ=255)
                                           tgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAACAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCa                                                                                <  2:456329/140‑1 (MQ=255)
                                                aatgTGAAGATAAACAGTGCTGCTAAAGTAACTTTCACATCTAAATAGAATATTATGTATAGTGCATTAATAATTGTTATATATTCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatc                                                                           <  1:140818/140‑1 (MQ=255)
                                                aatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATTGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatc                                                                           <  1:496769/140‑1 (MQ=255)
                                                aatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatc                                                                           <  2:186262/140‑1 (MQ=255)
                                                aatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatc                                                                           <  2:594515/140‑1 (MQ=255)
                                                aatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTAAATAATCTAACAAATCATTCCT‑TAACCAGGTTAAAATGAAATCTTTTGTTTGTTCAAcata                                                                           >  1:252891/1‑139 (MQ=255)
                                                  tgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatcat                                                                         <  2:511334/140‑1 (MQ=255)
                                                  tgGGAAGAGAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatcat                                                                         <  2:149307/140‑1 (MQ=255)
                                                    ggAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTa                                                                       >  2:664117/1‑140 (MQ=255)
                                                        gATAAATAGTTCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCa                                                                   <  2:213162/140‑1 (MQ=255)
                                                        gATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCa                                                                   <  1:347337/140‑1 (MQ=255)
                                                        gATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCa                                                                   <  1:614699/140‑1 (MQ=255)
                                                         aTAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCAc                                                                  >  1:426226/1‑140 (MQ=255)
                                                            aaCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCActct                                                               >  2:226799/1‑140 (MQ=255)
                                                             aCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTa                                                              <  1:570719/140‑1 (MQ=255)
                                                             aCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAACCTTTTGTGTTTTCAACATCATTAATCACTCTa                                                              <  2:142902/140‑1 (MQ=255)
                                                                  gctgctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCACCATCATTAATCACTCTAGctat                                                         >  2:270386/1‑140 (MQ=255)
                                                                  gctgctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGatat                                                         >  1:156040/1‑140 (MQ=255)
                                                                    tgctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATCGTGCAATACTAATTGTTATATAATCTAACAAAAAATTCATCTAAAGC‑CTAAAGAATAAATTTATTGTTTGTTCAACATCATTAATCACTCTAGATATTa                                                       >  1:289323/1‑140 (MQ=255)
                                                                    tgctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATATTTTGTTTGTTAAACATCATTAATCACTCTAGATATTa                                                       >  1:93209/1‑140 (MQ=255)
                                                                          aGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGAc                                                 >  1:472206/1‑140 (MQ=255)
                                                                                                aaCATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACGCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTAGTAGCATaaaa                           <  1:483461/140‑1 (MQ=255)
                                                                                                  cATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAAtc                         >  2:105072/1‑140 (MQ=255)
                                                                                                   aTTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAAtct                        >  2:375436/1‑140 (MQ=255)
                                                                                                    ttATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTCAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAAtctc                       <  2:476545/140‑1 (MQ=255)
                                                                                                    ttAGGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTCAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTTCTTGATTATTAGCATAAAAtctc                       <  2:476621/140‑1 (MQ=255)
                                                                                                         gATAGTTCAATAATAATTGTTATATAATCTAGCCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTATTTAACATCATTAAGCACTCTTGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACt                  <  2:202/140‑1 (MQ=255)
                                                                                                           tAGTGCAATAATAAATGTTATATAATCTAACCAGATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCTTTAATTACTCTAGTTATTACTTGACCTACTTGATTATCAGCATAAAATCTCGCACTTa                <  1:405445/140‑1 (MQ=255)
                                                                                                            aGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTTTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACttca               >  1:663415/1‑138 (MQ=255)
                                                                                                             gTGCAATAATAATTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTaaa              >  2:564519/1‑140 (MQ=255)
                                                                                                                cAATAATAATTGTTATATAATCTAACCAAATATTCCT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAATCt           >  1:396239/1‑140 (MQ=255)
                                                                                                                       aatTGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAAt    >  1:627532/1‑140 (MQ=255)
                                                                                                                         ttGTTATATAATCTCACCAAATATTCAA‑TAATCTGGTTAACATGAAATCTTTTGTTTGTTCAACATCATTAATCCCTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATgg  >  2:276813/1‑140 (MQ=255)
                                                                                                                         ttGTTATATAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATAACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATgg  >  1:218607/1‑140 (MQ=255)
                                                                                                                                 |                                                                                                                                    
GTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCAT‑TAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGG  >  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