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 F59 I1 R1 22 28.7 559496 97.2% 543830 149.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP000730 1,188,185 C→T R140C (CGC→TGC)  pbpA → penicillin‑binding protein 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,188,1850CT100.0% 84.1 / NA 26R140C (CGC→TGC) pbpApenicillin‑binding protein 1
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (18/8);  total (18/8)

AAGGCGAGTGCCAATTCTAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGACGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCAAATGGCAATTTTGCATCACACTTAATTGGTAGAGCTCAGAAAAATC  >  CP000730/1188041‑1188329
                                                                                                                                                |                                                                                                                                                
aaGGCGAGTGCCAATTCTAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCaa                                                                                                                                              >  2:277614/1‑149 (MQ=255)
   gCGAGTGCCAATTCTAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAgg                                                                                                                                           >  1:207348/1‑149 (MQ=255)
   gCGAGTGCCAATTCTAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATATACAGTCATTAATATGAAGCAAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGAAAAgg                                                                                                                                           >  1:97152/1‑149 (MQ=255)
    cGAGTGCCAATTCTAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGa                                                                                                                                          >  1:243408/1‑149 (MQ=255)
     gAGTGCCAATTCTAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGaa                                                                                                                                         >  1:117448/1‑149 (MQ=255)
                 tAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGt                                                                                                                             >  2:14606/1‑149 (MQ=255)
                 tAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGt                                                                                                                             >  1:244839/1‑149 (MQ=255)
                 tAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGt                                                                                                                             >  2:14617/1‑149 (MQ=255)
                    aaaaCCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATc                                                                                                                          >  2:261223/1‑149 (MQ=255)
                       aCCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAgg                                                                                                                       <  1:65324/149‑1 (MQ=255)
                       aCCTAGGCATGTAGTTAATAAAAAAGAGACTGAAAAGAAATTATCTACAGTAATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAgg                                                                                                                       <  1:33916/149‑1 (MQ=255)
                           aGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACaa                                                                                                                   <  2:59667/149‑1 (MQ=255)
                                      agATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATGGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATag                                                                                                        <  2:60648/148‑1 (MQ=255)
                                                        aaaGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTg                                                                                      <  1:213496/149‑1 (MQ=255)
                                                        aaaGAAATTATCTACAGTCATTAACATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTg                                                                                      <  2:214997/149‑1 (MQ=255)
                                                                   cTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTa                                                                           >  2:49556/1‑149 (MQ=255)
                                                                    tACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTACAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTGTttatttat                                                                          >  2:60244/1‑149 (MQ=255)
                                                                                   gAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAAc                                                           >  1:137486/1‑149 (MQ=255)
                                                                                    aaGCCAGAGCAAACTGAAAATAGACTTAGTTAAAAGAAAGCCTTCCAATTTGAATTTTGATGCAAAGGTACAAATTTAACGTATCAGTACAAATTGAAAATAGAGAAAATGAATTTGCCTGCTACTTCTTTATTGCCTGAAACAGAACg                                                          >  2:30275/1‑149 (MQ=255)
                                                                                              aaaTTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCa                                                >  1:237993/1‑149 (MQ=255)
                                                                                                                    aaagaaagCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCAAATGGCAATTTTGCATCACACt                          <  1:3035/149‑1 (MQ=255)
                                                                                                                       gaaagCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCAAATGGCAATTTTGCATCACACTTaa                       >  1:71234/1‑149 (MQ=255)
                                                                                                                       gaaagCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCAAATGGCAATTTTGCATCACACTTaa                       >  1:277503/1‑149 (MQ=255)
                                                                                                                           gCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCAAATGGCAATTTTGCATCACACTTAATTgg                   >  2:124899/1‑149 (MQ=255)
                                                                                                                            cTTTCCAAATTGAATTTGGTTGCAAAGCACCAAAAATAACGTCTCAGGACAACTTGTAAATAAAGAAAATGAATATGCCTGGTATTTCTTTATTACCGGAAACAAAACGCTTTTATCCAAATGGCAATTTAGCATCATACTTAATTGGt                  >  2:27979/1‑149 (MQ=255)
                                                                                                                                            tGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCAAATGGCAATTTTGCATCACACTTAATTGGTAGAGCTCAGAAAAATc  <  2:117448/149‑1 (MQ=255)
                                                                                                                                                |                                                                                                                                                
AAGGCGAGTGCCAATTCTAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGACGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCAAATGGCAATTTTGCATCACACTTAATTGGTAGAGCTCAGAAAAATC  >  CP000730/1188041‑1188329

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ 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