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 I195 R1 222 27.1 1551108 96.0% 1489063 86.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 3,098,336 Δ1 bp coding (545/1080 nt) mltC → membrane‑bound lytic murein transglycosylase MltC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,098,3350C.100.0% 63.5 / NA 16coding (544/1080 nt)mltCmembrane‑bound lytic murein transglycosylase MltC
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (5/11);  total (5/11)

CTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATG  >  NZ_CP009273/3098250‑3098410
                                                                                     |                                                                           
cTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGcgaac                                                                         <  2:444753/90‑5 (MQ=255)
    gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                    <  2:116079/90‑1 (MQ=255)
                  gAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgcg                                                      <  2:365366/90‑1 (MQ=255)
                  gAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgcg                                                      <  2:626640/90‑1 (MQ=255)
                            cTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATAtc                                            >  2:411662/1‑90 (MQ=255)
                                    ccGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATg                                    <  1:283857/90‑1 (MQ=255)
                                     cGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATgg                                   <  1:641250/90‑1 (MQ=255)
                                      gcagcaACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGt                                  >  2:370158/1‑90 (MQ=255)
                                               ggCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGc                         <  2:490044/90‑1 (MQ=255)
                                                 cTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGt                       >  1:106511/1‑90 (MQ=255)
                                                  tGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTc                      <  2:445401/90‑1 (MQ=255)
                                                    cGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCAc                    <  2:9841/90‑1 (MQ=255)
                                                    cGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTAGGCATGGTCCGCCAGGCGTCAc                    <  1:36951/90‑1 (MQ=255)
                                                               cAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGc         >  2:91686/1‑90 (MQ=255)
                                                                   gTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtg     >  2:505277/1‑90 (MQ=255)
                                                                     cACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtgat   <  2:435349/90‑1 (MQ=255)
                                                                      aCCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtgatg  <  2:455332/90‑1 (MQ=255)
                                                                                     |                                                                           
CTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATG  >  NZ_CP009273/3098250‑3098410

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ 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
CCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGATTCT  >  NZ_CP009273/3098286‑3098423
                                                  |                                                                                       
CCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGG                                       <  SRR3722073.289868/100‑1 (MQ=60)
 CGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGC                                      <  SRR3722073.654482/100‑1 (MQ=60)
   cgtcggcagcgtcagatgtgtataagagacagCCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGT                                    <  SRR3722073.506164/68‑1 (MQ=60)
   CAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGT                                    >  SRR3722073.108815/1‑100 (MQ=60)
                CGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTAGGCATGGTCCGCCAGGCGTCACGGAAATATGG                       <  SRR3722073.37865/100‑1 (MQ=60)
                                   CCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGATT    >  SRR3722073.620492/1‑100 (MQ=60)
                                   CCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGGCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGATT    >  SRR3722073.314039/1‑100 (MQ=60)
                                     ATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGATTCT  >  SRR3722073.578652/1‑100 (MQ=60)
                                                  |                                                                                       
CCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGATTCT  >  NZ_CP009273/3098286‑3098423

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑