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
A13 F68 I0 R1 25 50.4 1217238 93.3% 1135683 133.9

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% 75.2 / NA 29C146Y (TGT→TAT) USA300HOU_RS10125Putative multidrug export ATP‑binding/permease protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (15/14);  total (15/14)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGT  >  USA300TCH1516_ALE/2010236‑2010488
                                                                                                                               |                                                                                                                             
cAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGTGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTCAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTa                                                                                                                         >  1:494837/1‑134 (MQ=255)
        ttAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAata                                                                                                                 >  1:514051/1‑134 (MQ=255)
             tttCCAACGAATACGTACTGCGTTAAAATGTTATAGGGTAAGTTAAACCGTGCTGCTAAAGTCAATTACACATCTTAATAGAACATAATGCATAGTGCAATAATATTTGTTATTTAATCTAACCAAATATTCAt                                                                                                            <  2:61348/133‑1 (MQ=255)
             cTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAt                                                                                                            >  1:188196/1‑134 (MQ=255)
             cTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCACAAATCAATTTCACATCTAAAAAGAACATAATGAACAACACAATAATAATTGGTATATAATCTAACCAAATCTTCAt                                                                                                            >  2:588180/1‑134 (MQ=255)
                ccAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGATATATAATCTAACCAAATATTCATTaa                                                                                                         >  2:158893/1‑134 (MQ=255)
                     gAAAACGTACACCGTTAAAATGTAAAATAGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGGTAGTGCAATAACAATTGTACTATACACTAACCAAATATTAATCAACACgc                                                                                                    >  2:127166/1‑133 (MQ=255)
                              caacGTTAAAATGTAAAATAGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATATAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGa                                                                                           <  1:112571/131‑1 (MQ=255)
                                 cGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATTAAAt                                                                                        >  1:248477/1‑134 (MQ=255)
                                        atgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttgt                                                                                 >  2:501928/1‑134 (MQ=255)
                                                 gggAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAc                                                                        <  2:374146/134‑1 (MQ=255)
                                                    aaGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATAAACAAGGTTAAAATGAAATCTTTTATTTCTTCacaaga                                                                     >  2:381871/1‑129 (MQ=255)
                                                        tAAACAGTGCTGCTAAAGTCAATTTCACAGCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTa                                                                 <  1:552283/134‑1 (MQ=255)
                                                          aaCAGTGCTGCGAAAGGCAATTACACATCTAAAAATAACATTATGGATAGTGCAATAATAATTGTTATATAACCTAACGGAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAAt                                                               <  2:101140/134‑1 (MQ=255)
                                                             aGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCAc                                                            >  2:541133/1‑134 (MQ=255)
                                                             aGTGCTGCTAAAGTCAATTTAACATCTCAAAAGAACAATATGGATAGTGCAATAATAATTGTTATATAATCCAACCAAATATGCATTAACACGGTTAAAATGAAATCTTTTGTTTGTTCAACATAATTAATCAc                                                            >  2:528569/1‑134 (MQ=255)
                                                                     tAAAGTCAATTTCACATCTAAAAATAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGata                                                    <  1:3227/134‑1 (MQ=255)
                                                                                          aaaGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGattat                               >  2:573960/1‑134 (MQ=255)
                                                                                                cATTATGGATAGTGCAAGAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCAt                         <  2:385251/134‑1 (MQ=255)
                                                                                                  ttATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATaa                       <  1:249224/134‑1 (MQ=255)
                                                                                                   tgtGGATACTGCAATAATAATTGTTCTATAATCTAACCAAATATTCATTAACCCTGTTAAAATGAAATCTTTTTTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATaaa                      <  2:570496/132‑1 (MQ=255)
                                                                                                   taaggATAGCTCAATAATAATTGTTATATAATTTAACCAAATATTCATTAACCCGGTTAATAGGAAATCTTTTGGTTGGTCAACATCATTAAGTACTCTAGATACTACTTGACCTACTTGATTATTAGCATaaa                      <  2:76804/131‑1 (MQ=255)
                                                                                                      agATACTGCAATTATATTTGTTATATAATCTATCCAAATATTCATTAACCCGGTTAAAATTAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAAtc                   <  2:520495/133‑1 (MQ=255)
                                                                                                       gATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAAtct                  <  1:513284/134‑1 (MQ=255)
                                                                                                             gCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACt            <  2:438105/134‑1 (MQ=255)
                                                                                                             gCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACt            <  2:341925/134‑1 (MQ=255)
                                                                                                                     aatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTAAACATCATTAATCACTCTAGATATTACTTGACCAACTAGATTATTAGAATAAAATCGAGAACTTAAAGCta    >  2:255605/1‑133 (MQ=255)
                                                                                                                       ttGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGt  >  2:61463/1‑134 (MQ=255)
                                                                                                                       ttGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGATTGTAAAAAATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGt  >  1:48639/1‑134 (MQ=255)
                                                                                                                               |                                                                                                                             
CAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGT  >  USA300TCH1516_ALE/2010236‑2010488

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