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 I0 R1 35 35.7 768239 98.7% 758251 140.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,544,339 C→T 100% 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_ALE2,544,3390CT96.7% 81.4 / ‑3.5 31V189V (GTC→GTT) hlgC_2Gamma‑hemolysin component C
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (14/15);  total (15/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.29e-01
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.

TCAGCCCCATCACTCGGTGGTAATGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTCAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTCCAGACAGTGAGTTAC  >  USA300TCH1516_ALE/2544220‑2544460
                                                                                                                       |                                                                                                                         
tCAGCCCCATCACTCGGTGGTAATGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCAc                                                                                                       >  1:196217/1‑140 (MQ=255)
tCAGCCCCATCACTCGGTGGTAATGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAAAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCAc                                                                                                       >  1:196266/1‑140 (MQ=255)
       cATCACTCGGTGGTAATGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCa                                                                                                >  1:763804/1‑140 (MQ=255)
               ggtggtAATGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAATGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCaaaa                                                                                        >  1:102719/1‑140 (MQ=255)
                  ggtAATGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAATTCCTTTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATc                                                                                     <  1:593727/140‑1 (MQ=255)
                      aTGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGcc                                                                                 >  1:97324/1‑140 (MQ=255)
                      aTGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGcc                                                                                 <  1:570877/140‑1 (MQ=255)
                                tAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCg                                                                       >  1:457593/1‑140 (MQ=255)
                                 aaCTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGa                                                                      <  1:602261/140‑1 (MQ=255)
                                 aaCTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGAATAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGa                                                                      >  1:593619/1‑140 (MQ=255)
                                       tCTAAATCGATTATCTTTCCACAACAAAATTATGTAAGTGAAGTATAATTACTTCACTCTTAAAGTGTTTTATGGGGCGTTAAAGTGAATTTATTCGTCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGatttatt                                                                <  1:674583/140‑1 (MQ=255)
                                               gATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCt                                                        <  1:681061/140‑1 (MQ=255)
                                                aTTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTa                                                       <  1:341838/140‑1 (MQ=255)
                                                  tAGCTATACAAAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTCAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACa                                                     <  1:430247/140‑1 (MQ=255)
                                                       ataCACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAACGAATTCATTCGCCACTAAATAAGGTCAAAAAGCAGCCATTGATAGCGGTTTATTTGTAGCCTACAAACCt                                                >  1:236726/1‑140 (MQ=255)
                                                          cacaACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCAt                                             >  1:601352/1‑140 (MQ=255)
                                                          cacaACAAAATTATGTAAGAGAAATAGAACAACAAAACTCAAAAATTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCAt                                             <  1:479847/140‑1 (MQ=255)
                                                               caaAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGATAAAGCGAATTCATTCGCCACTGACTCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTAATAGTaa                                        >  1:394676/1‑140 (MQ=255)
                                                                  aaTTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGa                                     >  1:683837/1‑140 (MQ=255)
                                                                        gTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCAag                               >  1:541926/1‑140 (MQ=255)
                                                                             tGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGatt                          <  1:266139/140‑1 (MQ=255)
                                                                               aaGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGattat                        <  1:585225/140‑1 (MQ=255)
                                                                                 gTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTAttt                      <  1:453969/140‑1 (MQ=255)
                                                                                   aGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTAtttgg                    >  1:167556/1‑138 (MQ=255)
                                                                                   aGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCg                    >  1:278019/1‑140 (MQ=255)
                                                                                     aacaacAAAACTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGtt                  >  1:729092/1‑140 (MQ=255)
                                                                                             aaCTCAAAAAGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTCCAGACAg          <  1:436829/140‑1 (MQ=255)
                                                                                                  aaaaaGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTCCAGACAGTGAGt     <  1:615296/140‑1 (MQ=255)
                                                                                                   aaaaGTGTTTGATGGGTCGTTAACGCGAAGGCATCCGCCACTGCTTGCTTACAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTCCAGACAGTGAGtt    <  1:172952/140‑1 (MQ=255)
                                                                                                     aaGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTCCAGACCGTGAGTTac  <  1:560930/140‑1 (MQ=255)
                                                                                                     aaGTGTTTTATGGGGCGTTAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTCCAGACAGTGAGTTac  <  1:333763/140‑1 (MQ=255)
                                                                                                                       |                                                                                                                         
TCAGCCCCATCACTCGGTGGTAATGGATCATTTAACTATTCTAAATCGATTAGCTATACACAACAAAATTATGTAAGTGAAGTAGAACAACAAAACTCAAAAAGTGTTTTATGGGGCGTCAAAGCGAATTCATTCGCCACTGAATCAGGTCAAAAATCAGCCTTTGATAGCGATTTATTTGTAGGCTACAAACCTCATAGTAAAGATCCTAGAGATTATTTCGTTCCAGACAGTGAGTTAC  >  USA300TCH1516_ALE/2544220‑2544460

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A