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
A0 F0 I1 R1 155 25.8 2285122 88.0% 2010907 104.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA AM260479 2,907,333 Δ1 bp coding (209/1221 nt) h16_A2693 → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AM2604792,907,3320A.100.0% 53.1 / NA 13coding (208/1221 nt)h16_A2693conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (7/6);  total (7/6)

CCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGC  >  AM260479/2907213‑2907411
                                                                                                                       |                                                                               
ccgccgGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCt                                                                 <  1:536918/133‑1 (MQ=255)
                            cgtagtCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCgg                                    >  1:533619/6‑134 (MQ=255)
                                gtCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc                                           >  1:833084/2‑123 (MQ=255)
                                gtCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc                                           <  2:833084/122‑1 (MQ=255)
                                                              gagCAGTACGAGCTGAGCTTCTGGGAATCGATCGAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTggcggc  >  2:912406/1‑134 (MQ=255)
                                                                gCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTg                               <  1:555887/103‑1 (MQ=255)
                                                                gCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTg                               >  2:555887/1‑103 (MQ=255)
                                                                                 tCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCt        >  1:306795/1‑109 (MQ=255)
                                                                                 tCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCt        <  2:306795/109‑1 (MQ=255)
                                                                                  cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc                                           <  1:1062359/73‑1 (MQ=255)
                                                                                  cTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc                                           >  2:1062359/1‑73 (MQ=255)
                                                                                                            tATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc                                           >  1:537740/1‑48 (MQ=37)
                                                                                                            tATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGc                                           <  2:537740/48‑1 (MQ=37)
                                                                                                                       |                                                                               
CCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGC  >  AM260479/2907213‑2907411

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCACCGCCGCCCCGCTCCGGCACC  >  AM260479/2907201‑2907466
                                                                                                                                    |                                                                                                                                     
ggctcggagatgtgtataagagacaGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGC                                                                                                                   <  GWNJ‑0478:712:GW2002102894th:2:2210:9759:10430/125‑1 (MQ=60)
CGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGC                                                                                                                   <  GWNJ‑0478:712:GW2002102894th:2:2215:14534:64105/150‑1 (MQ=60)
        gtttatttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCC                                                                                                            <  GWNJ‑0478:712:GW2002102894th:2:2112:13863:41671/67‑1 (MQ=34)
           GCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAA                                                                                                         <  GWNJ‑0478:712:GW2002102894th:2:1214:5917:12828/149‑1 (MQ=60)
            ttttgtttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagtctgggaatcgatcaagAACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAA                                                                                                         <  GWNJ‑0478:712:GW2002102894th:2:1114:18029:84478/50‑1 (MQ=46)
                         gcttcaggtaggcctcgtagTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGT                                                                                          >  GWNJ‑0478:712:GW2002102894th:2:1215:1437:96508/21‑150 (MQ=60)
                             caggtaggcctcgtagTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTG                                                                                      >  GWNJ‑0478:712:GW2002102894th:2:2114:4839:86950/17‑150 (MQ=60)
                                gagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCC                                                                                   <  GWNJ‑0478:712:GW2002102894th:2:2213:3283:7477/103‑1 (MQ=60)
                                            atgtgtataagagacagCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGccgctccagg                                                                       <  GWNJ‑0478:712:GW2002102894th:2:1216:14185:4308/133‑11 (MQ=60)
                                               agcgagtgtctcgtgggctcggagatgtgtataagagacagGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAG                                                                    <  GWNJ‑0478:712:GW2002102894th:2:2202:11076:54007/109‑1 (MQ=60)
                                                                         GGAGCAGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaa                                           >  GWNJ‑0478:712:GW2002102894th:2:1112:15847:48419/1‑77 (MQ=53)
                                                                              AGTACGAGCTGAGCTTCTGGGAATCGATCAAG‑AACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCtgtctcttat                                     >  GWNJ‑0478:712:GW2002102894th:2:1203:11235:54862/1‑140 (MQ=60)
                                                                                                         atcaagAACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaa            >  GWNJ‑0478:712:GW2002102894th:2:1214:3837:16521/7‑78 (MQ=60)
                                                                                                             agAACAGCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCACCGCCGCCCCGCTCCG       >  GWNJ‑0478:712:GW2002102894th:2:1113:17806:101256/3‑150 (MQ=60)
                                                                                                                   GCAATTATGCC‑GGCG‑ACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaa  >  GWNJ‑0478:712:GW2002102894th:2:1108:6603:14967/1‑68 (MQ=60)
                                                                                                                                    |                                                                                                                                     
CGGCCGCCGCTGCCGCCGGCCCCGCGGCCACGGAACCGCTGCTGCTCGCCGGCATCATGCCCAAGAACACCGAGGAGCAGTACGAGCTGAGCTTCTGGGAATCGGACAAGAAACAGCAATTATGCCGGGCGAACTACGAGGCCTACCTGAAGCAGTACCCCAACGGACGCTTCGCGGTGCTGGCCAGGGCGCGCCTGGAGCGGCTGGCGGCGTCCGCCTCCGCACCCAAGGCCCAGGCGCCCGCACCGCCGCCCCGCTCCGGCACC  >  AM260479/2907201‑2907466

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑