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 I200 R1 216 30.8 1683622 97.2% 1636480 87.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
ACTTATACGCTGGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTGTTACCGCAGCAACCT  >  NZ_CP009273/1877718‑1877913
                                                                                                  |                                                                                                 
ACTTATACGCTGGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTC                                                                                                  >  SRR3722079.183723/1‑100 (MQ=60)
ACTTATACGCTGGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTAATGCTGCTATTACCGGCGTCC                                                                                                  >  SRR3722079.734895/1‑100 (MQ=60)
 CTTATACGCTGGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCG                                                                                                 >  SRR3722079.16287/1‑100 (MQ=60)
 CTTATACGCTGGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCG                                                                                                 >  SRR3722079.67070/1‑100 (MQ=60)
 CNTATACGCTGGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCG                                                                                                 >  SRR3722079.620183/1‑100 (MQ=60)
   TATACGCTGGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCC                                                                                               <  SRR3722079.338761/100‑1 (MQ=60)
                    AATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCGCCCGCAAGGCCCATGGGGA                                                                              >  SRR3722079.719160/1‑100 (MQ=60)
                                           TGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCT                                                       <  SRR3722079.527148/100‑1 (MQ=60)
                                               GAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATC                                                   >  SRR3722079.12736/1‑100 (MQ=60)
                                                          GTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGG                                        >  SRR3722079.340146/1‑100 (MQ=60)
                                                                         GCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTC                         >  SRR3722079.712655/1‑100 (MQ=60)
                                                                         GCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTC                         <  SRR3722079.798690/100‑1 (MQ=60)
                                                                           ATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCC                       <  SRR3722079.842679/100‑1 (MQ=60)
                                                                                     CTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTGTTAC             <  SRR3722079.714538/100‑1 (MQ=60)
                                                                                      TATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTGTTACC            <  SRR3722079.142394/100‑1 (MQ=60)
                                                                                                GTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTGTTACCGCAGCAACCT  <  SRR3722079.309088/100‑1 (MQ=60)
                                                                                                  |                                                                                                 
ACTTATACGCTGGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTGTTACCGCAGCAACCT  >  NZ_CP009273/1877718‑1877913

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑