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 F124 I0 R1 39 155.3 7715808 93.9% 7245143 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,168,372 G→C 100% noncoding (1/76 nt) gltT → tRNA‑Glu

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,168,3720GC45.6% ‑7.0 / 2.4 6noncoding (1/76 nt)gltTtRNA‑Glu
Reads supporting (aligned to +/- strand):  ref base G (0/2);  new base C (0/2);  total (1/5)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.35e-01

ATAAGGCCGTTCGCTTTCTATTAATGAAAGCTCACCCTACACGAAAATATCACGCAACGCGTGATAAGCAATTTTCGTGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTT  >  NC_000913/4168294‑4168457
                                                                              |                                                                                     
atacgcccGTTCGCTTTCTATTAATGAAAGCTCACCCTACACGAAAATATCACGCAACGCGTGATAAGCAATTTTCGTGTCCCCTTCGTCTAGAGGccc                                                                   <  1:674351/93‑1 (MQ=0)
   agtccGTTCGCTTTCTATTAATGAAAGCTCACTCTACACGAAAATATCACGCAACGCGTGATAAGCAATTTTCGTGTCCCCTTCGTCTAGAGGCCCa                                                                  <  1:1788722/94‑1 (MQ=0)
                        tgataactgaCCCTACGCGCAACTAGCTCTCCACGCGTAATAACCCATTCCCTTCTCCCCGTCGTCTCGATCCTGAGCACACCGCCCTTTCAcggcgg                                            <  1:663382/89‑1 (MQ=0)
                                     tatacGAAAATATCACGCAACGCGTGATAAGCAATTTTCGGCTCCCCTTCGGCTAGAGGCCCAGGTCACCGCGCTTTCACGGCGGTAACAGGGGTTCGaa                             <  2:3567635/97‑1 (MQ=1)
                                      acactagagtatCACGCAAGCCGTGATAAGAAATTTTCGTTGCCCCTTCGTCTAGGGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGTTCGaa                             <  1:3686023/90‑1 (MQ=1)
                                                                tacgCAATTTTCGTATCCCCTTCGTCTAGAGGCCCTGGACACCACCCTCTCACGGCTGTAACAGGGGTTCGAATCCCCGAGGGGACGCCACTTGCTGGtg  >  1:3603482/4‑99 (MQ=1)
                                                                              |                                                                                     
ATAAGGCCGTTCGCTTTCTATTAATGAAAGCTCACCCTACACGAAAATATCACGCAACGCGTGATAAGCAATTTTCGTGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTT  >  NC_000913/4168294‑4168457

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A