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
A3 F60 I1 R1 14 18.2 455004 92.7% 421788 134.9

Breseq alignment

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

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,513,9300AT87.5% 15.9 / ‑6.1 8L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base T (3/4);  total (4/4)
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

TTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAA  >  USA300TCH1516_ALE/1513827‑1514032
                                                                                                       |                                                                                                      
ttGGCATGGGGTTTGTCTCTTGGATAAAGCTTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATAACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                         >  1:29921/1‑135 (MQ=255)
 tGGCATGGGGTGTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                        <  2:3173/135‑1 (MQ=255)
   gCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGAt                                                                      <  1:43733/135‑1 (MQ=255)
        gggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAATACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCTATTATTTGGATTTTcg                                                                 >  1:160256/1‑134 (MQ=255)
            ttGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                             >  2:100966/1‑135 (MQ=255)
                                           tGCAATAAAAGTACAACATTGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtata                              <  2:188316/135‑1 (MQ=255)
                                                                 gTAAAAAAACAAACATCTAAATAACTCATAATATATTTAATTGTATTAGGATTATTAATACCATTATTTGAATTATCACTTATCCTCTTACTTATAATTGAATTAATATTATATATTAAAAATAGTCTTGCTaat        >  2:124256/1‑134 (MQ=255)
                                                                       aaaCCATCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGTATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataa  <  1:146804/135‑1 (MQ=255)
                                                                                                       |                                                                                                      
TTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAA  >  USA300TCH1516_ALE/1513827‑1514032

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A