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 F42 I1 R1 60 69.9 3000528 98.3% 2949519 146.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947_CJ‑RC 4,741,338 C→G intergenic (+468/+285) 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‑RC4,741,3380CG97.4% 136.7 / ‑3.3 39intergenic (+468/+285)gltA/yeiWcitrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base G (25/13);  total (26/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

GCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AACCTCCGCCAACTGCAATTCGTGAACCAAGCAAAAGGCCCCGAAAAGGCCCTC‑C‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCA  >  NC_002947_CJ‑RC/4741232‑4741470
                                                                                                           |                                                                                                                                      
gCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCgga                                                                                              >  1:122593/1‑147 (MQ=255)
gCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCgga                                                                                              <  2:12462/149‑3 (MQ=255)
   tcctTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCggaca                                                                                            >  8:185082/1‑144 (MQ=255)
     ctTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCggacacgt                                                                                         <  3:270108/149‑8 (MQ=255)
     ctTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCggacacgt                                                                                         >  3:266853/1‑142 (MQ=255)
             tCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGtcctc‑ctgc                                                                                <  3:8442/149‑4 (MQ=255)
             tCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGtcctc‑ctg                                                                                 >  1:288458/1‑146 (MQ=255)
               gTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGtcctc‑ctgca                                                                               <  5:178146/148‑5 (MQ=255)
                 aaTGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGtcctc‑c                                                                                   >  6:177612/1‑142 (MQ=255)
                 aaTGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGcg                                                                            >  2:357949/1‑148 (MQ=255)
                         gcaCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGATACGTCCTC‑CTGCAGcgcctcgacc                                                                    >  3:252012/1‑143 (MQ=255)
                                     gcggcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGtcctc‑ctgca                                                                               >  4:109286/1‑122 (MQ=255)
                                     gcggcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGtcctc‑ctgca                                                                               <  3:109286/126‑5 (MQ=255)
                                     gcggcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAgcggc                                                        >  1:280520/1‑149 (MQ=255)
                                     gcggcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAgcggc                                                        <  1:318576/149‑1 (MQ=255)
                                           tCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCtt                                                   >  1:93311/1‑148 (MQ=255)
                                             aCCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGa                                                 >  4:88593/1‑148 (MQ=255)
                                                   cATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACgg                                           <  8:48703/148‑1 (MQ=255)
                                                       gCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTCAT‑GCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTcaca                                      >  6:104473/1‑149 (MQ=255)
                                                           aTTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACcgc                                  >  1:303048/1‑149 (MQ=255)
                                                               aaCTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGa                                >  5:21347/1‑147 (MQ=255)
                                                                 cTGGGTATAGGTCAAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTCAT‑GCAGCGCCTCGACCTTGGCCAGCGCAGCCTTGATCACGGACACACCGCGATAgg                            >  4:64301/1‑149 (MQ=255)
                                                                     gTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCtt                        >  1:224841/1‑149 (MQ=255)
                                                                     gTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCtt                        <  3:219397/149‑1 (MQ=255)
                                                                     gTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCtt                        <  2:52736/149‑1 (MQ=255)
                                                                        taGGTCCAGCTCTGTTCACCTTCGTGCTTGAGCAGCTTATGCGAATTGC‑ATTCGTGAATCCAGGCACAGGCACAGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCAAGGTCACACCGAGATAGTCCttt                       >  8:19352/1‑146 (MQ=255)
                                                                        taGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGt                      >  8:154305/1‑148 (MQ=255)
                                                                           gTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt                  >  5:137579/1‑149 (MQ=255)
                                                                           gTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACt                   >  8:56821/1‑148 (MQ=255)
                                                                            tCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt                  <  7:270904/148‑1 (MQ=255)
                                                                            tCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTg                 <  1:357949/149‑1 (MQ=255)
                                                                             ccAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTg                 >  1:273699/1‑148 (MQ=255)
                                                                               aGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAc              >  3:256318/1‑149 (MQ=255)
                                                                                gCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAc              <  8:371486/148‑1 (MQ=255)
                                                                                  tctGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCg           >  2:123339/1‑149 (MQ=255)
                                                                                      gTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCa       >  3:77225/1‑149 (MQ=255)
                                                                                       tCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCgg          <  7:31678/145‑1 (MQ=255)
                                                                                         aCCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCt    >  2:177729/1‑149 (MQ=255)
                                                                                           cTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTC‑CTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCa  >  2:112907/1‑149 (MQ=255)
                                                                                                           |                                                                                                                                      
GCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AACCTCCGCCAACTGCAATTCGTGAACCAAGCAAAAGGCCCCGAAAAGGCCCTC‑C‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCA  >  NC_002947_CJ‑RC/4741232‑4741470

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A