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
A9 F174 I0 R1 34 41.4 875437 98.7% 864056 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,513,930 A→T 100% L413F (TTA→TTT)  USA300HOU_RS07375 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,513,9300AT96.3% 79.6 / ‑3.6 27coding (1239/1341 nt)USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (13/13);  minor base . (1/0);  total (14/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

GTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAAC  >  USA300TCH1516_ALE/1513806‑1514051
                                                                                                                             |                                                                                                                         
ggatCGATGTATTATTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGAATTCATCGCACGGCAATAAAAGTACCCCATCGCGTAACAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGattat                                                                                                           <  1:412734/139‑1 (MQ=255)
  atCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGAttatta                                                                                                         >  1:799120/1‑141 (MQ=255)
         tattaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCCCATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGGATTAGGATTATTAATGCCat                                                                                                  >  1:662109/1‑141 (MQ=255)
          attaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCAatt                                                                                                 >  1:635182/1‑141 (MQ=255)
            tagtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATCT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGACattat                                                                                               >  1:425200/1‑141 (MQ=255)
            tagtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattat                                                                                               >  1:510237/1‑141 (MQ=255)
            tagtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattat                                                                                               >  1:441344/1‑141 (MQ=255)
                agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                           <  1:59335/141‑1 (MQ=255)
                    cttGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTa                                                                                       <  1:27283/140‑1 (MQ=255)
                    cttGGCATGGGGTTTGTCTCTTGGATAAAGCGAACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTa                                                                                       <  1:28617/140‑1 (MQ=255)
                    aTTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACCGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTa                                                                                       <  1:202965/141‑1 (MQ=255)
                        gCATGGGGTTTGTCTCTTCGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCAc                                                                                   <  1:315894/141‑1 (MQ=255)
                         cATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACt                                                                                  <  1:35103/141‑1 (MQ=255)
                          aTGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCACGTAAAAAAACCAGCATCTATATCCACTTATTGACTGTGT‑ATTGTATTAGGATTATTAATGCCATAATTTGGATTATCACtt                                                                                 >  1:853300/1‑141 (MQ=255)
                                      tctTGGATAAAGCGTACAAAAAAAACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAttt                                                                     <  1:778327/141‑1 (MQ=255)
                                        ttGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTtat                                                                   <  1:170368/141‑1 (MQ=255)
                                                       aaaaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtatt                                                    <  1:35666/141‑1 (MQ=255)
                                                         aaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtattat                                                  <  1:677520/141‑1 (MQ=255)
                                                         aaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtattat                                                  >  1:780310/1‑141 (MQ=255)
                                                                   caTAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTATTGCCATTATTTGGATTTTCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGa                                        <  1:385121/140‑1 (MQ=255)
                                                                   aaTAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGa                                        <  1:385127/141‑1 (MQ=255)
                                                                    aTAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAt                                       >  1:556078/1‑141 (MQ=255)
                                                                    aTAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGGTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAATTATAATTGAATTAATATTATATATTAAAgct                                       >  1:583601/1‑139 (MQ=255)
                                                                         aGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTTAATTAATATTATATATTAAAGAtcgtct                                  >  1:257787/1‑140 (MQ=255)
                                                                              cacaTCGCGTAAAAATACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTa                             >  1:649203/1‑141 (MQ=255)
                                                                                  tCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTAGTGCTAAACa                         >  1:694620/1‑141 (MQ=255)
                                                                                                         tat‑CACTCATAATATGTTTTATTGGATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAAc  >  1:553566/1‑141 (MQ=255)
                                                                                                                             |                                                                                                                         
GTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATAT‑CACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAAC  >  USA300TCH1516_ALE/1513806‑1514051

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A