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
A9 F110 I1 R1 27 18.3 392680 99.5% 390716 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,028,269 G→C P126A (CCA→GCA)  USA300HOU_RS10230 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,028,2690GC100.0% 71.0 / NA 19P126A (CCA→GCA) USA300HOU_RS10230hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (10/9);  total (10/9)

ACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACG  >  USA300TCH1516_ALE/2028144‑2028399
                                                                                                                             |                                                                                                                                  
aCCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCAcc                                                                                                                     <  1:163893/141‑1 (MQ=255)
            tCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTg                                                                                                         >  1:257461/1‑141 (MQ=255)
             cTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGt                                                                                                        <  1:110559/141‑1 (MQ=255)
                 caacaaTGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTtaa                                                                                                    <  1:156719/141‑1 (MQ=255)
                       tGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAg                                                                                              >  1:154449/1‑141 (MQ=255)
                        ggTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGa                                                                                             >  1:233614/1‑141 (MQ=255)
                             tattTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTg                                                                                        <  1:36327/141‑1 (MQ=255)
                                     ttAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATa                                                                                >  1:251452/1‑141 (MQ=255)
                                              gCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTCCGTTGCTAACAAACACGCTATGCCATTGTAAAAGATTTTGAAGTCATAACCTCAGcc                                                                       >  1:76207/1‑141 (MQ=255)
                                              gCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATcc                                                                       >  1:377653/1‑141 (MQ=255)
                                                       gTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAact                                                              >  1:173513/1‑141 (MQ=255)
                                                        ttAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAacta                                                             >  1:271063/1‑141 (MQ=255)
                                                              cAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACttttt                                                       >  1:327393/1‑141 (MQ=255)
                                                                            ccAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTtg                                         >  1:19230/1‑141 (MQ=255)
                                                                                ttCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTa                                     <  1:57103/141‑1 (MQ=255)
                                                                                   cATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTa                                  <  1:47711/141‑1 (MQ=255)
                                                                                   cATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTa                                  <  1:47819/141‑1 (MQ=255)
                                                                                              tGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGcaca                       <  1:220325/141‑1 (MQ=255)
                                                                                                                   aCATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACg  <  1:361492/141‑1 (MQ=255)
                                                                                                                             |                                                                                                                                  
ACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACG  >  USA300TCH1516_ALE/2028144‑2028399

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A