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 I74 R1 158 13.7 815430 95.7% 780366 86.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,671,899 T→G T88P (ACG→CCG)  pntA ← Re/Si‑specific NAD(P)(+) transhydrogenase subunit alpha

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,671,8990TG100.0% 14.9 / NA 6T88P (ACG→CCG) pntARe/Si‑specific NAD(P)(+) transhydrogenase subunit alpha
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (2/4);  total (2/4)

CATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGA  >  NZ_CP009273/1671816‑1671946
                                                                                   |                                               
cATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc                                           <  1:266108/90‑1 (MQ=255)
  tCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAg                                         >  2:123632/1‑90 (MQ=255)
              tCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACg                             <  1:324664/90‑1 (MQ=255)
                        ttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcatc                   <  1:123632/90‑1 (MQ=255)
                                  ttttGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGgc         >  2:28088/1‑90 (MQ=255)
                                         ttAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGa  <  2:390825/90‑1 (MQ=255)
                                                                                   |                                               
CATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGA  >  NZ_CP009273/1671816‑1671946

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
AGAGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTTCTACAATTTCAGC  >  NZ_CP009273/1671810‑1671998
                                                                                         |                                                                                                   
AGAGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGA                                                                                           <  SRR3722212.107856/100‑1 (MQ=60)
      CATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGT                                                                                     <  SRR3722212.269532/100‑1 (MQ=60)
                    TCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATC                                                                       <  SRR3722212.329133/100‑1 (MQ=60)
                              TTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGC                                                             <  SRR3722212.125059/100‑1 (MQ=60)
                                                                                         GTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTTCTACAATTTCAGC  >  SRR3722212.96113/1‑100 (MQ=60)
                                                                                         |                                                                                                   
AGAGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTTCTACAATTTCAGC  >  NZ_CP009273/1671810‑1671998

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑