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
A5 F71 I1 R1 31 24.1 564604 94.3% 532421 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,698,127 C→T G480G (GGC→GGT)  copA → Copper‑exporting P‑type ATPase A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,698,1270CT100.0% 54.3 / NA 20G480G (GGC→GGT) copACopper‑exporting P‑type ATPase A
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (12/8);  total (12/8)

CATTTGAACCTGCACTTGTTGCGAGTATTTCCGTTCTCGTCATTGCTTGTCCATGCGCATTGGGACTTGCTACACCAACTTCTATTATGGTAGGTACTGGTCGCGCTGCTGAAAATGGTATTTTATTTAAAGGTGGCGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACGGGTACCATTACAAATGGTCGTCCAGTCGTGACAGATTATCATGGTGACAATCAAACGCTACAACTACTTGCTACTGCTGAAA  >  USA300TCH1516_ALE/2697991‑2698260
                                                                                                                                        |                                                                                                                                     
cATTTGAACCTGCACTTGTTGCGAGTATTTCCGTTCTCGTCATTGCTTGTCCATGCGCATTGGGACTTGCTACACCAACTTCTATTATGGTAGGTACTGGTCGCGCTGCTGAAAATGGTATTTTATTTAAAGGTGGTGAGt                                                                                                                                   <  1:73668/141‑1 (MQ=255)
                                      gTCATTGCTTGTCCATGCGCATTGGGACTTGCTACACCAACTTCTATTATGGTAGGTACTGGTCGCGCTGCTGAAAATGGTATTTTATTTAAAGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTa                                                                                             >  1:277388/1‑141 (MQ=255)
                                             cTTGTCCATGCGCATTGGGACTTGCTACACCAACTTCTATTATGGTAGGTACTGGTCGCGCTGCTGAAAATGGTATTTTATTTAAAGGTGGTGAGTTTGTTTAACGCACACATCAAATTAATACTATCCTTTTATATAAGa                                                                                      >  2:181395/1‑141 (MQ=255)
                                                     tGCGCATTGGGACTTGCTACACCAACTTCTATTATGGTAGGTACTGGTCGCGCTGCTGAAAATGGTATTTTATTTAAAGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACAGGTAcc                                                                              >  2:191892/1‑141 (MQ=255)
                                                      gcgcATTGGGACTTGCTACACCAACTTCTATTATGGTAGGTACTGGTCGCGCTGCTGAAAATGGTATTTTATTTAAAGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACGGGTACCa                                                                             >  2:251817/1‑141 (MQ=255)
                                                       cgcATTGGGACTTGCTACACCAACTTCTATTATGGTAGGTACTGGTCGCGCTGCTGAAAATGGTCTTTTATTTAAAGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACGGGTAGCAt                                                                            >  1:156710/1‑141 (MQ=255)
                                                                 cTTGCTACACCAACTTCTAATATGGTAGGTACTGGTCGCGCTGCTGAAAATGGTATTTTATTTAAAGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGGTAAGACGGATACAAGTAAAAATGgt                                                                  >  2:83472/1‑141 (MQ=255)
                                                                   tGCTACACCAGCTTCTATTATGGTACGTACTGGTCGCGCTGCTGAAAATGGTATTTTATTTAAAGGTGGTGAGTTTGTTGCGTCCCGACGTTAAATTGATACCATCGTTTTAGATAAGACGGGTACCATTACAAATGgtcg                                                                <  1:252460/141‑1 (MQ=255)
                                                                                tCTATTATGGTAGGTACTGGTCGCGCTGCTGAAAATGGTATTTTATTTAAAGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACGGGTACCATTACAAATGGTCGTCCAGTCGTGACa                                                   >  1:14517/1‑141 (MQ=255)
                                                                                   agtatGTTGGGTACTGGTCGCGCTACTGAAAATGGTATTTTATTTAAAGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACGGGTACCATTACAAATGGTCGTCCAGTCGTGACAGAt                                                <  1:69937/139‑1 (MQ=255)
                                                                                    ttatGGTAGGTACTGGTCGCGCTGCTGAAAATGGTATTTTATTTAAAGGTGGTGAGTTGGTTGAACGCACAAATCAAATTGATACCATCGTTTTAGATAAGACGGGTACCATTACAACTGGTCGTCCAGTCCTGACAGAtt                                               >  2:213703/1‑141 (MQ=255)
                                                                                           aggtaCTGGTCGCGCTGCTGAAAATGGTATTTTATTTAAAGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACGGGTACCATTACAAATGGTCGTCCAGTCGTGACAGATTATCATgg                                        >  2:203834/1‑141 (MQ=255)
                                                                                           aggtaCTGGTCGCGCGGCTGAAAATGGTATTTTATTTAAAGGTGGTGAATTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACGGGTACCATTACAAATGGTCGTCCAGTCGTGACAGCTTATCATgg                                        >  2:202848/1‑141 (MQ=255)
                                                                                             gtaCTGGTCGCGCTGCTGAAAATGGTATTTTATTTAAAGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACGAGTACCATTACAAATGGTCGTCCAGTCGTGAAAGATTATCATGGTg                                      >  2:111456/1‑141 (MQ=255)
                                                                                                tggggcgcgATGTTGAAAATGTTATTTTATTTAAAGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACAATCGTTTTAGATAAGACGGGTACCATTACAAATGGTCGTCCAGTCGTGACAGATTATCATGGTGACa                                   <  2:160595/136‑1 (MQ=255)
                                                                                                        gctgctGAAAATGGTATTTTATTTAAAGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACGTGTACCATTACAAATGGTCGTCCAGTCGTGACAGATTATCATGGTGACAATCAAACg                           <  1:3673/141‑1 (MQ=255)
                                                                                                         ctgctgAAAATGGTATTTTATTTAAAGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACGGGTACCATTACAAATGGTCGTCCAGTCGTGACAGATTATCATGGTGACAATCAAACGc                          <  1:136412/141‑1 (MQ=255)
                                                                                                          tgctgAAAATGGTATTTTATTTAAAGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACGGGTACCATTACAAATGGTCGTCCAGTCGTGACAGATTATCATGGTGACAATCAAACGCt                         <  1:187548/141‑1 (MQ=255)
                                                                                                                               taAAGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACGCGTACCATTACAAATGGTCGTCCAGTCGTGACAGATTATCATGGTGACAATCAAACGCTACAACTACTTGCTACTGCTGa    <  2:220998/141‑1 (MQ=255)
                                                                                                                                 aaGGTGGTGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACGGGTACCATTACAAATGGTCGTCCAGTCGTGACAGATTATCATGGTGACAATCAAACGCTACAACTACGTGCTACTGCTGaaa  >  1:231882/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                     
CATTTGAACCTGCACTTGTTGCGAGTATTTCCGTTCTCGTCATTGCTTGTCCATGCGCATTGGGACTTGCTACACCAACTTCTATTATGGTAGGTACTGGTCGCGCTGCTGAAAATGGTATTTTATTTAAAGGTGGCGAGTTTGTTGAACGCACACATCAAATTGATACCATCGTTTTAGATAAGACGGGTACCATTACAAATGGTCGTCCAGTCGTGACAGATTATCATGGTGACAATCAAACGCTACAACTACTTGCTACTGCTGAAA  >  USA300TCH1516_ALE/2697991‑2698260

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