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
A5 F24 I1 R1 57 68.7 2934938 98.3% 2885044 146.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947_CJ‑RC 4,741,381 A→C intergenic (+511/+242) 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‑RC4,741,3810AC96.9% 110.4 / ‑6.4 32intergenic (+511/+242)gltA/yeiWcitrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base C (21/10);  total (21/11)
Fisher's exact test for biased strand distribution p-value = 3.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGAACCTCCGCCAACTGCAATTCGTGA‑ACCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTT  >  NC_002947_CJ‑RC/4741254‑4741518
                                                                                                                                |                                                                                                                                          
gcagcaCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGcgcctc                                                                                                                        >  5:302436/1‑146 (MQ=255)
               gcggcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAgcggc                                                                                                        >  4:222643/1‑149 (MQ=255)
                    gTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCtt                                                                                                   >  7:119635/1‑149 (MQ=255)
                           gCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACg                                                                                            <  8:208413/149‑1 (MQ=255)
                           gCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACg                                                                                            <  5:268646/149‑1 (MQ=255)
                                  cGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCacac                                                                                     >  8:23491/1‑149 (MQ=255)
                                    tATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACcg                                                                                   >  6:22402/1‑149 (MQ=255)
                                            tGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGc                                                                           >  3:322208/1‑149 (MQ=255)
                                              ggTATTGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGATTCCAGGCAGAGGGCCCGGTCACGTCCTCCT‑GCTGCGCCTCGACCTTGGCCAGCGGAGCCTTGATCACGGTCACACCGCGTTAGGcc                                                                          <  2:309245/148‑1 (MQ=255)
                                                 acaGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCGGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTg                                                                       >  3:30852/3‑148 (MQ=255)
                                                     gTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt                                                                  >  5:110896/1‑149 (MQ=255)
                                                     gTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt                                                                  <  5:262904/149‑1 (MQ=255)
                                                      tCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTg                                                                 >  2:312868/1‑149 (MQ=255)
                                                                gTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCa                                                       >  2:361645/1‑149 (MQ=255)
                                                                gTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCa                                                       >  7:317730/1‑149 (MQ=255)
                                                                 tCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCAc                                                      >  8:264658/1‑149 (MQ=255)
                                                                 tCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCAc                                                      >  6:159932/1‑149 (MQ=255)
                                                                 tCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCAc                                                      >  8:150527/1‑149 (MQ=255)
                                                                   aCCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCt                                                    >  7:325824/1‑149 (MQ=255)
                                                                     cTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCa                                                  <  8:308043/149‑1 (MQ=255)
                                                                      ttCGTGCTTGAGCAGCTTCTGCGACTCGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCAc                                                 >  6:203378/1‑149 (MQ=255)
                                                                                             tcttgcaTTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgtc                           <  7:344519/142‑1 (MQ=255)
                                                                                                 gcaTTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgtcctc                        <  6:302436/145‑1 (MQ=255)
                                                                                                 gcaTTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgtc                           >  8:344519/3‑144 (MQ=255)
                                                                                                   aTTCGTGA‑ATCCAGGCACAGGCCTCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgtcctcgtcc                    >  3:149970/1‑149 (MQ=255)
                                                                                                               caggcacaGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACtt          <  1:168085/141‑1 (MQ=255)
                                                                                                                aggcacaGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGc        >  7:283944/7‑149 (MQ=255)
                                                                                                                aggcacaGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGc        <  7:264658/143‑1 (MQ=255)
                                                                                                                aggcacaGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGc        <  1:128461/143‑1 (MQ=255)
                                                                                                                  gcacaGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCa      <  8:317730/145‑1 (MQ=255)
                                                                                                                    acaGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGt    >  4:13135/3‑149 (MQ=255)
                                                                                                                       ggCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACAGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGttt  >  4:84435/1‑148 (MQ=255)
                                                                                                                                |                                                                                                                                          
GCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGAACCTCCGCCAACTGCAATTCGTGA‑ACCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTTT  >  NC_002947_CJ‑RC/4741254‑4741518

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