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
A1 F2 I194 R1 197 32.2 1845014 95.2% 1756453 85.4

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TGATTTTCGACGTTGGCAAGCTGATGGATGCCTTTATGGAAGCCGATACCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGCCGAGGT  >  NZ_CP009273/3138677‑3138842
                                                                                       |                                                                              
TGATTTTCGACGTTGGCAAGCTGATGGATGCCTTTATGGAAGCCGATACCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACAC                                                                    <  SRR3722072.501808/100‑1 (MQ=60)
 GATTTTCGACGTTGGCAAGCTGATGGATGCCTTTATGGAAGCCGATACCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACACC                                                                   >  SRR3722072.441444/1‑100 (MQ=60)
               GCAAGCTGATGGATGCCTTTATGGAAGCCGATACCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCTCCGGCCACACACCGCCAACATCGCAGA                                                     <  SRR3722072.742382/100‑1 (MQ=60)
                 AAGCTGATGGATGCCTTTATGGAAGCCGATACCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAAT                                                   <  SRR3722072.231173/100‑1 (MQ=60)
                              CCTTTATGGAAGCCGATACCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCTCCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGC                                      >  SRR3722072.231798/1‑100 (MQ=60)
                                           agatgtgtataagagacagGCCATAGCAAGGGTGACCAATCGCCTCCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGT                         <  SRR3722072.684565/81‑1 (MQ=60)
                                                  TTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGC                  <  SRR3722072.41870/100‑1 (MQ=60)
                                                         TTACAGCCATAGCAAGGGTGACCAATCGCCTCCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTAC           <  SRR3722072.676177/100‑1 (MQ=60)
                                                                  TAGCAAGGGTGACCAATCGCCTCCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGctgtctcttatacacatctccgagccca  >  SRR3722072.862552/1‑72 (MQ=60)
                                                                  TAGCAAGGGTGACCAATCGCCTCCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGCCGAGGT  >  SRR3722072.724416/1‑100 (MQ=60)
                                                                  TAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGCCGAGGT  >  SRR3722072.118757/1‑100 (MQ=60)
                                                                                       |                                                                              
TGATTTTCGACGTTGGCAAGCTGATGGATGCCTTTATGGAAGCCGATACCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGCCGAGGT  >  NZ_CP009273/3138677‑3138842

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑