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 5,196,590 T→G 17.6% intergenic (+29/+24) PP_4574 → / ← PP_4575 hypothetical protein/urea amidolyase‑like protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC5,196,5900TG17.6% 40.8 / 8.5 34intergenic (+29/+24)PP_4574/PP_4575hypothetical protein/urea amidolyase‑like protein
Reads supporting (aligned to +/- strand):  ref base T (15/13);  new base G (2/4);  total (17/17)
Fisher's exact test for biased strand distribution p-value = 6.56e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.08e-01

CCAAGCAGGCCTGGGAGTACACCGCCTCGACCCATCTGGTGCGCGACCTGATCGAGGACAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGTCCCCGGCATGCACTGCGCCAGTTGCGCCAGCGCCAGCGGCGTCAGCG  >  NC_002947_CJ‑RC/5196443‑5196738
                                                                                                                                                   |                                                                                                                                                    
ccAAGCAGGCCTGGGAGTACACCGCCTCGACCCATCTGGTGCGCGACCTGATCGAGGACAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTc                                                                                                                                                     <  3:170798/149‑1 (MQ=255)
  aaGCAGGCCTGGGAGTACACCGCCTCGCCCCATCTGGTGCGCGACCTGATCTAGGACAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTCAGGTTGCATGTACCGGCCCATTCGCGGGCtag                                                                                                                                                    >  8:415853/1‑146 (MQ=255)
      aGGCCTGGGAGTACACCGCCTCGACCCATCTGGTGCGCGACCTGATCGAGGACAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTCGCCcgc                                                                                                                                               <  3:28587/149‑1 (MQ=255)
           tGGGAGTACACCGCCTCGACCCATCTGGTGCGCGACCTGATCGAGGACAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTAGCGGGCTCGCCCGCGa                                                                                                                                             >  8:63478/1‑146 (MQ=255)
               aGTACACCGCCTCGACCCATCTGGTGCGCGACCTGATCGAGGACAAGATTTATCCGCTGACCCTGCATGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGc                                                                                                                                       <  6:328236/148‑1 (MQ=255)
                  acacCGCCTCGACCCATCTGGTGCGCGACCTGATCGAGGACAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGCcag                                                                                                                                    >  6:99659/1‑148 (MQ=255)
                       gCCTCGACCCATCTGGTGCGCGACCTGATCGAGGACAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGCCAGCAGTc                                                                                                                               >  6:373070/1‑148 (MQ=255)
                        ccTCGACCCATCTGGTGCGCGACCTGATCGAGGACAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTAGCGGGCTCGCCCCCCAAACGGCCAGCAGTCt                                                                                                                              >  5:207061/1‑148 (MQ=255)
                         cTCGACCCATCTGGTGCGCGACCTGATCGAGGACAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGCCACCAGTCt                                                                                                                              >  8:414366/1‑147 (MQ=255)
                         cTCGACCCATCTGGTGCGCGACCTGATCGAGGACAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTAGCCCGCGAAAGGGCcagcactac                                                                                                                              >  8:303338/1‑143 (MQ=255)
                                        gcgcGACCTTTTCGAGTACATTATGTATCCGCTCACCCTGCATGGTTTGGAGGACGGGATGCGCTACCTGTCAAAGTGAGGTTGCCTGTCCCGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGCCAGCAGTCTTACGACCAACGCCCCa                                                                                                              <  6:232969/148‑1 (MQ=255)
                                        gcgcGACCTGATCGAGGACAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGCCAGCAGTCTTACGACCAACGCCCCAg                                                                                                             <  2:230673/149‑1 (MQ=255)
                                             aCCTGATCGAGGACAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGCCAGCAGTCTTACGACCCACGCCCCAGGTa                                                                                                          >  6:73062/1‑147 (MQ=255)
                                                    cGAGGACAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAgctgct                                                                                                  >  6:188622/1‑148 (MQ=255)
                                                         aCAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGCCCGCAGTCTTACGACCCACGCCCCAGGTAAAGCTGCAGctct                                                                                             >  6:114622/1‑148 (MQ=255)
                                                         aCAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTAGCGGGCTCGCCCGCCAAAGGGCCAGCCGTCTTTAGACCAACGCCCCCGGTAAAactgctgctgt                                                                                             >  6:314829/1‑146 (MQ=255)
                                                            aGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTAGCGGGCGAGCCCGCGCAACGGCCAGCCCTGTTTCCACCCACGCCCCAGGTAAAgcagctgctatagc                                                                                          >  7:237676/1‑143 (MQ=255)
                                                              aTGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAg                                                                                       <  2:235586/149‑1 (MQ=255)
                                                                   tCCGCTTACCCTGCATGGTTTGTTGGAGGGTATGCGCTACCTGTCCATGTGAGGTTGCCTGTACCGGCCCTTTGGCGGGCTCGCCCGCTAATGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCt                                                                                   <  8:237676/148‑1 (MQ=255)
                                                                      gCTCACCCTGCATGGGTTGGAGGACGGGATGCGCTACCTGTCCATGTGTGTTTGCCTTTACCGCCCCTTTCGCGGGCTCGCCCGCTAATGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTc                                                                               <  2:120458/149‑1 (MQ=255)
                                                                         gACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTGCCGGCCCTATCGCGGGCTCGGCCGCGGAAGGGCCAGCCGGCTTACGACCACCGCGCCAGGTAAAGGGGCTGCTCTCGCCAGGCCTCGTccgg                                                                            >  2:217128/1‑147 (MQ=255)
                                                                              tGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCATTAGCGGGCTCGCCCGCGAAAGGGGCCGCCGTCTTACGACCCACCCCCCAGGGAAAGCTGCTGCTCTCGCCCGGCCTCGTCCAGcccc                                                                        >  8:365282/1‑148 (MQ=255)
                                                                                                         cccTGTCCATGTGCGGTGGCCTGACCCGCCCATTTCGCGGGCGCGCCCGCTAATGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGTcccc                                             <  5:73062/147‑1 (MQ=255)
                                                                                                          ccTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGTccc                                              <  5:188622/146‑1 (MQ=255)
                                                                                                           cTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTAGCGGGCTCGCCCGCGAAAGGGCCCGCAGTATTAAGACCAACGCCCCAGGTAAAGCTGCTGCGCTAGCCAGGCCAACTCCAGCACCACCGCCCAGAACCGCCCCAACCTCCCCGGc                                          >  2:100716/1‑149 (MQ=255)
                                                                                                                  tgtgtGGTTGCCTGTCCCGCCCCTTCCGCGGGCGCGCCGGCTAATGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGTCCCCGGCATGCACt                                   <  4:214782/148‑1 (MQ=255)
                                                                                                                  cgggcggTGGCCTGTCCCGGCCATTGCGCGGGCGCGCCCGCGAATGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGTCCCCGGCATGCAc                                    <  5:306642/143‑1 (MQ=255)
                                                                                                                        gtggCCTGTCCCGGCCCTTTCGCGGGCTCGCCCGCGAATGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGTCCCCGGCATGCACTGCGcc                              <  5:114622/145‑1 (MQ=255)
                                                                                                                             cTGTACCGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGTCCCCGGCATGCACTGCGCCAGTTg                         <  5:99659/148‑1 (MQ=255)
                                                                                                                                   cGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGTCCCCGGCATGCACTGCGCCAGTTgcgccagc                  <  2:119065/149‑1 (MQ=255)
                                                                                                                                         tttCGCGGGCGAGCCCGCGAAAGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGTCCCCGGCATGCACTGCGCCAGTTGCgccagcgccagc            >  1:351479/1‑149 (MQ=255)
                                                                                                                                            cgcgGGCTCGCCCGCTAAAGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGTCCCCGGCATGCACTGCGCCAGTTGCGCCAGCGCCAgcggc         <  1:100716/149‑1 (MQ=255)
                                                                                                                                             gcgGGCTCGCCCGCGAAAGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGACCCCGGCATGCACTGCGCCAGTTGCGCCAGCGCCAgcggcg        >  4:341099/1‑149 (MQ=255)
                                                                                                                                             gcgGGCGAGCCCGCGAAAGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGTCCCCGGCATGCACTGCGCCAGTTGCGCCAGCGCCAgcggc         <  2:351479/148‑1 (MQ=255)
                                                                                                                                                ggCTCGCCCGCGAAAGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGTCCCCGGCATGCACTGCGCCAGTTGCGCCAGCGCCAGCGGCGTcc     >  1:179606/1‑148 (MQ=255)
                                                                                                                                                   tCGCCCGCGAAAGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGTCCCCGGCATGCACTGCGCCAGTTGCGCCAGCGCCAGCGGCGTCAgcg  >  4:379803/1‑149 (MQ=255)
                                                                                                                                                   |                                                                                                                                                    
CCAAGCAGGCCTGGGAGTACACCGCCTCGACCCATCTGGTGCGCGACCTGATCGAGGACAAGATGTATCCGCTGACCCTGCAAGGGTTGGAGGACGGGATGCGCTACCTGTCCAAGTGAGGTTGCCTGTACCGGCCCTTTCGCGGGCTCGCCCGCGAAAGGGCCAGCAGTCTTACGACCAACGCCCCAGGTAAAGCTGCTGCTCTCGCCAGGCCTCGTCCTGCACCACCGCCCTGAACCGCACCACCGTCCCCGGCATGCACTGCGCCAGTTGCGCCAGCGCCAGCGGCGTCAGCG  >  NC_002947_CJ‑RC/5196443‑5196738

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A