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
A3 F14 I0 R1 206 76.7 3255580 98.8% 3216513 146.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947_CJ‑RC 4,741,362 C→T 100% intergenic (+492/+261) gltA → / ← yeiW citrate synthase/putative oxidoreductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC4,741,3620CT100.0% 134.1 / NA 40intergenic (+492/+261)gltA/yeiWcitrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (20/20);  total (20/20)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AACCTCCGCCAACTGCAATTCGTGAACCAAGCAAAAGGCCCCGAAAAGGCCCTC‑C‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGT  >  NC_002947_CJ‑RC/4741237‑4741498
                                                                                                                              |                                                                                                                                          
ctTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCggacac                                                                                                                       <  3:383827/147‑6 (MQ=255)
              tgtgCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGcgc                                                                                                       >  8:281374/1‑146 (MQ=255)
                tgCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGcgcct                                                                                                     <  7:312190/148‑2 (MQ=255)
                     caCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGGATAGGGCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGcgcctcgacc                                                                                                <  6:350741/148‑7 (MQ=255)
                             cACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAg                                                                                        >  8:404663/1‑148 (MQ=255)
                               cgcgGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAgcg                                                                                      >  6:248075/1‑148 (MQ=255)
                                 cggcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAgcggcg                                                                                   <  1:247163/149‑1 (MQ=255)
                                 cggcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAgcggc                                                                                    >  6:229476/1‑148 (MQ=255)
                                     gTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCtt                                                                               <  2:250564/149‑1 (MQ=255)
                                     gTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCt                                                                                <  7:98518/148‑1 (MQ=255)
                                      tCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCtt                                                                               >  2:22952/1‑148 (MQ=255)
                                        aCCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTg                                                                              <  6:147834/147‑1 (MQ=255)
                                        aCCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGa                                                                             >  2:383541/1‑148 (MQ=255)
                                        aCCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGa                                                                             <  6:317862/148‑1 (MQ=255)
                                        aCCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGGCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGAt                                                                            <  2:331876/149‑1 (MQ=255)
                                         ccGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGAt                                                                            >  8:411904/1‑148 (MQ=255)
                                               aTGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGt                                                                      <  5:202351/148‑1 (MQ=255)
                                                  gCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTcaca                                                                  <  3:295603/149‑1 (MQ=255)
                                                    gTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGCCACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCacac                                                                 >  6:298629/1‑148 (MQ=255)
                                                     tATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACcg                                                               >  3:123200/1‑149 (MQ=255)
                                                      aTTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACcg                                                               >  7:76458/1‑148 (MQ=255)
                                                          aaCTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGa                                                            <  7:411904/147‑1 (MQ=255)
                                                          aaCTGGGTATAGGTCCAGCACAGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACCTCCTC‑CTGCAGAGCCTCGACCATGGCCAGCTGCGCCATGATCACGGTCACACCGCGa                                                            >  2:206113/1‑147 (MQ=255)
                                                           aCTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGa                                                            >  6:303160/1‑146 (MQ=255)
                                                                gTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCtt                                                    >  1:279944/1‑149 (MQ=255)
                                                                gTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCt                                                     >  5:289783/1‑148 (MQ=255)
                                                                      gTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt                                              <  1:73865/149‑1 (MQ=255)
                                                                      gTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACt                                               <  5:219699/148‑1 (MQ=255)
                                                                         cAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTg                                             <  5:117920/147‑1 (MQ=255)
                                                                         cAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGa                                           <  3:100279/149‑1 (MQ=255)
                                                                               tGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGc                                     >  2:386262/1‑149 (MQ=255)
                                                                                ggTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGc                                     >  7:38469/1‑148 (MQ=255)
                                                                                 gTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGcc                                    <  6:289783/148‑1 (MQ=255)
                                                                                 gTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGcc                                    <  6:271155/148‑1 (MQ=255)
                                                                                  tCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCa                                   >  7:313558/1‑148 (MQ=255)
                                                                                      cTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCa                              <  2:86207/149‑1 (MQ=255)
                                                                                       ttCGTGCTTGAGCAGCTTCAGCGACATGC‑ATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTAGGACCCGGCCACCTCa                              >  8:405879/1‑148 (MQ=255)
                                                                                       ttCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTCAT‑GCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGAGATAGGCCTTGTACTTGGACCCGGCCACCTCa                              >  8:411544/1‑148 (MQ=255)
                                                                                                              gacttgcaTTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgt        <  5:234170/141‑1 (MQ=255)
                                                                                                                   gcaTTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgtcctcgt  >  1:18649/3‑149 (MQ=255)
                                                                                                                              |                                                                                                                                          
CTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AACCTCCGCCAACTGCAATTCGTGAACCAAGCAAAAGGCCCCGAAAAGGCCCTC‑C‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGT  >  NC_002947_CJ‑RC/4741237‑4741498

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A