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
A7 F184 I1 R1 32 17.0 340811 99.5% 339106 149.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,544,339 C→T V189V (GTC→GTT)  hlgC_2 → Gamma‑hemolysin component C

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,544,3390CT100.0% 60.9 / NA 17V189V (GTC→GTT) hlgC_2Gamma‑hemolysin component C
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (12/5);  total (12/5)

GGATACAATATCGGTGGTAATTTCCAATCAGCCCCATCACTCGGTGGTAATGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTCAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTCCAGACAGTGAGTTACCACCTCTTGTACAAAGTG  >  USA300TCH1516_ALE/2544193‑2544478
                                                                                                                                                  |                                                                                                                                           
ggATACAATATCGGTGGTAATTTCCAATCAGCCCCATCACTCGGTGGTAATGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTaa                                                                                                                                           >  1:196851/1‑149 (MQ=255)
ggATACAATATCGGTGGTAATTTCCAATCAGCCCCATCACTCGGTGGTAATGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTaa                                                                                                                                           >  1:210/1‑149 (MQ=255)
                        cAATCAGCCCCATCACTCGGTGGTAATGGATCATTTAACGATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATc                                                                                                                   <  1:252437/149‑1 (MQ=255)
                                      aCTCGGTGGTAATGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAg                                                                                                     <  1:80396/149‑1 (MQ=255)
                                           gtggtAATGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCttt                                                                                                >  1:326697/1‑149 (MQ=255)
                                                                       aTCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAAc                                                                    >  1:34350/1‑149 (MQ=255)
                                                                             tAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATa                                                              <  1:296283/149‑1 (MQ=255)
                                                                                   taCACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAg                                                        >  1:65341/1‑149 (MQ=255)
                                                                                      acaacaAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATc                                                     >  1:83657/1‑149 (MQ=255)
                                                                                                      aGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGt                                     >  1:58696/1‑149 (MQ=255)
                                                                                                        tGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGCCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTc                                   <  1:176832/149‑1 (MQ=255)
                                                                                                          aaGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTCCa                                 >  1:14272/1‑149 (MQ=255)
                                                                                                            gTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTCCAGa                               >  1:108175/1‑149 (MQ=255)
                                                                                                             tAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTCCAGAc                              >  1:215035/1‑149 (MQ=255)
                                                                                                                aacaacAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGCTTTATTTGTAGGATCCACAGCTCATGGTAAAGATCCTAGAGATTATTTCGTTCCAGACAGt                           >  1:220500/1‑149 (MQ=255)
                                                                                                                         aCTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTCCAGACAGTGAGTTacca                  <  1:91371/149‑1 (MQ=255)
                                                                                                                                         aTGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTCCAGACAGTGAGTTACCACCTCTTGTACAAAGTg  >  1:126876/1‑149 (MQ=255)
                                                                                                                                                  |                                                                                                                                           
GGATACAATATCGGTGGTAATTTCCAATCAGCCCCATCACTCGGTGGTAATGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTCAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTCCAGACAGTGAGTTACCACCTCTTGTACAAAGTG  >  USA300TCH1516_ALE/2544193‑2544478

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A