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
A2 F1 I1 R1 748 32.0 1685426 92.6% 1560704 103.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,996,372 C→T *302* (TAG→TAA)  insD1 ← IS2 transposase TnpB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,996,3720CT95.2% 57.1 / ‑6.2 21*302* (TAG→TAA) insD1IS2 transposase TnpB
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (9/11);  total (10/11)
Fisher's exact test for biased strand distribution p-value = 4.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

AGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAA  >  NC_000913/2996254‑2996488
                                                                                                                      |                                                                                                                    
aGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGtt                                                                                                  >  1:203575/1‑139 (MQ=255)
 ttACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTa                                                                                                 <  2:203575/138‑1 (MQ=255)
    cATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCa                                                                                              >  1:557609/1‑139 (MQ=255)
                                                           aCAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCa                                       >  1:263734/1‑139 (MQ=255)
                                                                     aGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAAcc                                                                                       >  1:461900/1‑81 (MQ=255)
                                                                     aGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAAcc                                                                                       <  2:461900/81‑1 (MQ=255)
                                                                          aCAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTa                                                                                                 >  1:117640/1‑66 (MQ=255)
                                                                          aCAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTa                                                                                                 <  2:117640/66‑1 (MQ=255)
                                                                             gATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGcc                     <  1:152006/139‑1 (MQ=255)
                                                                             gATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGcc                     <  2:590780/139‑1 (MQ=255)
                                                                             gATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGcc                     <  1:396798/139‑1 (MQ=255)
                                                                             gATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGcc                     <  2:557609/139‑1 (MQ=255)
                                                                               tCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACAt                                                                                                       <  2:600577/55‑1 (MQ=255)
                                                                               tCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACAt                                                                                                       >  1:600577/1‑55 (MQ=255)
                                                                               tCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCGCGCTGCCGCAGATATTccc                                                         >  2:495042/1‑101 (MQ=255)
                                                                               tCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCg                                                                          <  1:149489/84‑1 (MQ=255)
                                                                               tCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCg                                                                          >  2:149489/1‑84 (MQ=255)
                                                                               tCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTccc                                                         <  1:495042/101‑1 (MQ=255)
                                                                               tCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCAt                   >  1:223857/1‑139 (MQ=255)
                                                                                 aaTGGAAGTAAATTCCAAATGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGGTATCTCTTAACCCATTACAAGCCAGCTGCCGCAGTTATTCCGGTGGCCAGCGATAACCCCGAGCACTATGCGGAGGCCATTc                 >  2:618794/1‑139 (MQ=14)
                                                                                                cAATTGTTTATTGGATTTGCCCTTATATTTACAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACGATGCGGATGCCATTCGTTATAATGCTCGaa  <  1:201031/139‑1 (MQ=255)
                                                                                                                      |                                                                                                                    
AGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAA  >  NC_000913/2996254‑2996488

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A