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
A23 F110 I0 R1 32 23.2 500348 95.1% 475830 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,483,375 G→T 76.2% V45F (GTC→TTC)  USA300HOU_2346 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,483,3750GT76.2% 24.4 / 4.9 20V45F (GTC→TTC) USA300HOU_2346hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (2/3);  new base T (11/4);  total (13/7)
Fisher's exact test for biased strand distribution p-value = 2.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAACCTATGATGAAACTCAATTTATTTATCAATGCAAATGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTAGTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACGACTT  >  CP000730/2483237‑2483497
                                                                                                                                          |                                                                                                                          
tAACCTATGATGAAACTCAATTTATTTATCAATGCAAATGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTc                                                                                                                          >  1:225230/1‑141 (MQ=255)
 aaCCTATGATGAAACTCAATTTATTTATCAATGCAAATGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCg                                                                                                                         >  1:221843/1‑141 (MQ=255)
          tgaAACTCAATTTATTTATCAATGCAAATGAGACGGAGTCTTATATTGGTATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAAGCACATACATTATTCGGAACCATaa                                                                                                                >  2:203107/1‑140 (MQ=255)
               cTCAATTTATTTATCAATGCAAATGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGCCaaa                                                                                                           >  1:75349/1‑141 (MQ=255)
                          tatCAATGCAAATGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTAGTCGGATACATAGACAAAGAAATCCatat                                                                                                >  2:243414/1‑141 (MQ=255)
                                                tCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGGCAAAGAAATCCATATCATTAATGTATCAGATGTtata                                                                          <  2:245737/141‑1 (MQ=255)
                                                  ttATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTAGTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAAc                                                                        <  1:72403/141‑1 (MQ=255)
                                                                     acTAAAATGAATGATAACGTTCGAAGTACTATTAATGCAGTAAATGCTTTACACAAATCACATTCACTAGTCAGATACATGGACAAAGAAATCCATATCATTATTGTATCAGATGTTATAACATTCCAAGTTATTAATaaa                                                     <  2:185991/140‑1 (MQ=255)
                                                                      cTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTAGTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATaaaa                                                    <  1:76086/141‑1 (MQ=255)
                                                                      cTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTAGTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATaaaa                                                    >  2:222087/1‑141 (MQ=255)
                                                                          aatgaatgATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGt                                                >  1:223850/1‑141 (MQ=255)
                                                                                       gTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCCTTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACa                                   >  2:26421/1‑141 (MQ=255)
                                                                                       gTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAAAAGCCATTACa                                   >  2:26293/1‑141 (MQ=255)
                                                                                                      aaTGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGACGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAACCAAAAATTc                    >  2:32777/1‑141 (MQ=255)
                                                                                                       aTGCAGTCAAGTCTTTACACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCa                   <  2:225230/141‑1 (MQ=255)
                                                                                                                aTGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAAt          <  2:221843/141‑1 (MQ=255)
                                                                                                                      tAGACAAATCACATACATTATTCGGATACATAGCCAAAGAAATCCATATGATTAATGTATCAGATGTTATAACATTCGACGGTATTAATTAAAATGTAACGGCCAGTACCAGCAATGAAAAATTACACCTCAAAttccacc    >  2:131054/1‑136 (MQ=255)
                                                                                                                        gACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACGACtt  >  1:104721/1‑141 (MQ=255)
                                                                                                                        gACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACAACtt  >  2:14878/1‑141 (MQ=255)
                                                                                                                        gACAAATCACATACAATATTAGGATAAATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACGACtt  <  2:156713/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                          
TAACCTATGATGAAACTCAATTTATTTATCAATGCAAATGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTAGTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACGACTT  >  CP000730/2483237‑2483497

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A