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 798,664 T→G 24.2% intergenic (+19/+8) fklB‑I → / ← PP_0685 FKBP‑type peptidyl‑prolyl cis‑trans isomerase/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC798,6640TG24.2% 46.3 / 4.9 36intergenic (+19/+8)fklB‑I/PP_0685FKBP‑type peptidyl‑prolyl cis‑trans isomerase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (22/4);  new base G (5/4);  total (28/8)
Fisher's exact test for biased strand distribution p-value = 1.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATGAACGCTGGCAGCAAATGGCGCCTGTACGTGCCAAGCGAGCTGGCTTACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACTCGAATTCAGCCCGCTCATGTCCAGGTCACCCTGGTCACGCAGTTCGTC  >  NC_002947_CJ‑RC/798518‑798812
                                                                                                                                                  |                                                                                                                                                     
tgatgaACGCTGGCAGCAAATGGCGCCTGTACGTGCCAAGCGAGCTGGCTTACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTg                                                                                                                                                      >  5:406261/1‑148 (MQ=255)
         cTGACAGCAAATGGCGCCTGTACGTGCCAAGCGAGCTGGCTTACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCAGGGCCGG‑CCTcc                                                                                                                                            <  8:201799/148‑2 (MQ=255)
          tGGCAGCAAATGGCGCCTGTACGTGCCAAGCGAGCTGGCTTACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCTCAAt                                                                                                                                          >  1:218134/1‑149 (MQ=255)
                caAATGGCGCCTGTACGTGCCAAGCGAGCTGGGTTACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGTGCTGCTCGAGGTTCTGTATTGCCCTGATGGCCGGCCGTGCGGG‑CGTCAATTCCAGt                                                                                                                                    <  2:130866/149‑1 (MQ=255)
                   aTGGCGCCTGTACGTGCCAAGCGAGCTGGCTTACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCTCAATTCCAGTCTg                                                                                                                                 >  4:220487/1‑149 (MQ=255)
                           tGTACGTGCCAAGCGAGCTGGCTTACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCGGCCGG‑CCGCAATTCCAGTCTGTcccccc                                                                                                                          >  7:18377/1‑148 (MQ=255)
                             tACGTGCCAAGCGAGCTGGCTTACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCGCAAATCCAGTCTGTcccccccg                                                                                                                        >  7:215502/1‑146 (MQ=255)
                                    cAAGCGAGCTGGCTTACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCCGCCCGGCCCG‑CCGCCAATGCACTCAGTACCCCCACGGCGCCAc                                                                                                                >  1:312460/1‑149 (MQ=255)
                                     aaGCGAGCTGGCTTACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCGCAATTCCAGTCTGTCCCCCCAGGGCGCAAc                                                                                                                >  5:233676/1‑148 (MQ=255)
                                      aGCGAGCTGGCTTACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACg                                                                                                               >  6:392740/1‑148 (MQ=255)
                                        cGAGCTGGCTTACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGACCTGGAGGCCGGCCCAGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGcc                                                                                                             >  8:2813/1‑148 (MQ=255)
                                             tGGCTTACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCCGCCCGGCCGG‑CCTCAATTACACTCTGTCCCCCCAGGGCGCAACGCCCccgc                                                                                                        >  2:168036/1‑148 (MQ=255)
                                                 ttACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCGGCCGG‑CCGCAATTCCAGTCTGTCCCCCCACGGCGCAACGCCCCCGCATAg                                                                                                    >  3:213685/1‑148 (MQ=255)
                                                  tACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAg                                                                                                    >  6:318452/1‑147 (MQ=255)
                                                       cgcCCATGGGTTTGGCCGCAGCCCCCCCCACCGCGTTGTGGTGTTCTAGGTCTCGCGGGTCTAGGTTGTTAAAGGCCCTGGCGGCGGGCCCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGcagaac                                                                                              <  8:215502/148‑1 (MQ=255)
                                                          ccAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCGCAATTCCAGTCTTTCCCCCCAGGGCGCAAAGCCCGCGCATAGcagaacaga                                                                                           >  4:22396/1‑148 (MQ=255)
                                                                       agcaTCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCGGCCGG‑CCTCAATTCCAGTCTGTCCCCCCCGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTAc                                                                             >  1:291610/1‑149 (MQ=255)
                                                                       agcaTCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCCGCCCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTAc                                                                             >  1:60454/1‑149 (MQ=255)
                                                                         caTCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCACGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTcc                                                                                 >  1:127873/1‑143 (MQ=255)
                                                                                  gcACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCTCAATTACACTCTGTCCCCCCCCGGCGCCACGCCCGCGCATAGCAGAACAGAAACAGAATACGTACCAGtagcgt                                                                    >  6:258214/1‑142 (MQ=255)
                                                                                                  ttCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCa                                                    >  6:32931/1‑147 (MQ=255)
                                                                                                  ttCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACt                                                  >  2:268705/1‑149 (MQ=255)
                                                                                                  ttCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCTCAAATCCAGTCTGTCCACCCAGGGCGCAACGCCCCCGCATAGCAGAACAGAAACAGAATCCGTACCAGATACGTGAGCACCCCCGGTTCAc                                                   >  8:388762/1‑148 (MQ=255)
                                                                                                         tCGAGCTGCTCGACGTTCTGTAAAGCCCTGGAGGCCCGCCCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCAAAGCAGAACAGAAACAGATAACCTACCACTTCCTTGAGCACCCCACGTACACTCGaaa                                             >  6:239424/1‑146 (MQ=255)
                                                                                                            tgctgctCTTGGTTTTTTAATGCCCTGGCGGGGGGCCCGGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACTCGAATTCAg                                         <  6:406261/147‑1 (MQ=255)
                                                                                                            aGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCCGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACTCGAATTAAg                                         >  5:282066/1‑148 (MQ=255)
                                                                                                            aGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCCGGGCGCAACGCCCCCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACTCGAATTCAg                                         >  7:174450/1‑148 (MQ=255)
                                                                                                                   cGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGGCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGGATAGCAGAACAGAAACAGAATCCCTACCAGTTCCTTGAGCACCCACGGTTCACTCGGATTAAGCCCGca                                   >  6:14670/1‑146 (MQ=255)
                                                                                                                           tGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGGTCACTCGAATTCAGCCCGCTCATGTCCAg                          >  7:415024/1‑148 (MQ=255)
                                                                                                                             tAATGCCCTGGAGGCCGGCCCTGGCGG‑CCTCAATTACAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACTCGAATTCAGCCCGCTCATGTCCAGGTc                       >  3:193090/1‑149 (MQ=255)
                                                                                                                                   cgtgtcggccggcctggccgg‑cctCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACTCGAATTCAGCCCGCTCATGTCCAGGTCACCCt                  <  8:335332/142‑1 (MQ=255)
                                                                                                                                    cTGGAGGCCGGCCCTGCCGG‑CCTCAATTCAAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACACAAACAGATTCCGTAACAGTTCCTTGAGCACCCCCGGATCAATCGAATTAAGCCCGCTCATGTCCAGGTCACACTg                 >  6:376866/1‑148 (MQ=255)
                                                                                                                                        cggcctgccGGGCGGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACTCGAATTCAGCCCGCTCATGTCCAGGTCACCCTGGTCAc            <  4:213685/148‑1 (MQ=255)
                                                                                                                                           ccggctTTGCCGG‑CCGCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACTCGAATTCAGCCCGCTCATGTCCAGGTCACCCTGGTCACGc          <  5:376866/148‑1 (MQ=255)
                                                                                                                                           ccggccCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACTCGAATTCAGCCCGCTCATGTCCa                           <  7:351257/131‑1 (MQ=255)
                                                                                                                                           ccggccCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACTCGAATTCAGCCCGCTCATGTCCa                           >  8:351257/1‑131 (MQ=255)
                                                                                                                                             ccccccGCCGGCCCGCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACTCGAATTCAGCCCGCTCATGTCCAGGTCACCCTGGTCACGCa         <  7:240137/146‑1 (MQ=255)
                                                                                                                                               cccGGCGGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACTCGAATTCAGCCCGCTCATGTCCAGGTCACCCTGGTCACGCAGtt      <  6:282066/148‑1 (MQ=255)
                                                                                                                                                  tGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACTCGAATTCAGCCCGCTCATGTCCAGGTCACCCTGGTCACGCAGTtcgtc  >  2:320262/1‑149 (MQ=255)
                                                                                                                                                  |                                                                                                                                                     
TGATGAACGCTGGCAGCAAATGGCGCCTGTACGTGCCAAGCGAGCTGGCTTACGGCGCCCAAGGCGTTGGCAGCATCCCGCCGCACAGCGTTCTGGTGTTCGACGTCGAGCTGCTCGACGTTCTGTAATGCCCTGGAGGCCGGCCCTGCCGG‑CCTCAATTCCAGTCTGTCCCCCCAGGGCGCAACGCCCGCGCATAGCAGAACAGAAACAGATTCCGTACCAGTTCCTTGAGCACCCCCGGTTCACTCGAATTCAGCCCGCTCATGTCCAGGTCACCCTGGTCACGCAGTTCGTC  >  NC_002947_CJ‑RC/798518‑798812

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