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
A10 F54 I0 R2 227 88.8 3424874 95.5% 3270754 127.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 3,476,692 G→T 31.6% H19N (CAT→AAT)  U712_17855 ← putative undecaprenyl‑phosphate galactose phosphotransferase‑like Protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,476,6920GT31.6% 53.6 / 9.0 50H19N (CAT→AAT) U712_17855putative undecaprenyl‑phosphate galactose phosphotransferase‑like Protein
Reads supporting (aligned to +/- strand):  ref base G (24/9);  new base T (5/11);  total (30/20)
Fisher's exact test for biased strand distribution p-value = 1.18e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGACGGATGTTAATTGGATGTAAA  >  CP006881/3476555‑3476829
                                                                                                                                         |                                                                                                                                         
cGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGt                                                                                                                                          <  1:181802/139‑1 (MQ=255)
    tcCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATTTAAAAGAATGTAttt                                                                                                                                      >  7:421263/1‑139 (MQ=255)
    tcCAAACAAATCAAAATTGAAAATACCGCAAACATTGGCAGCGCAATAGCCAATCCAATGAGCGCAAACCAAAAATCCATTACGCGCTTTAATGCCAAATAACGCGCCGTCTTTTGAGATAAAGTAAAAAAATATtttt                                                                                                                                      >  7:12325/1‑139 (MQ=255)
       aaacaaaTCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATttgtt                                                                                                                                   <  5:422761/139‑1 (MQ=255)
            aaTCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGATTGTATTTGTTGAACt                                                                                                                              <  6:69166/139‑1 (MQ=255)
             aTCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGCGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTg                                                                                                                             >  6:75180/1‑139 (MQ=255)
             aTCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTGGTTTGAGATTATGTAAAAGAATGTATTTGTTTATCTg                                                                                                                             >  7:174828/1‑139 (MQ=255)
                aaaaTTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTg                                                                                                                             >  4:407766/1‑136 (MQ=255)
                aaaaTTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAAAAAGTATTTGTTGAAcat                                                                                                                             >  4:384805/1‑134 (MQ=255)
                aaaaTTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCGTTTCAGATAATGTTAAAGAATGTATTTTTTGAACTg                                                                                                                             >  4:428604/1‑136 (MQ=255)
                aaaaTTGAAAATACCGCAATCATTGGCAGCGAAATCGCCAATCCAAAGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGACGTCGTTTCAGATAATTTATAAGAATTTATTTTTTGTACTg                                                                                                                             >  3:278114/1‑136 (MQ=255)
                              cGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAAATGAGAATTCACGACTcac                                                                                                             >  1:58987/1‑138 (MQ=255)
                                 aaTCATTGGCAGCGCAATCGCCAATCAAATGAGCCAAAACCAAATTTCAATTCCGCGATTATTTGACAAATCACGAGCCGTTTTTTCATATAATTTAATATATTTTTTTTTTTGAACTGACATTTCACGACTCACATTc                                                                                                         <  2:58987/139‑1 (MQ=255)
                                             cgcAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTGGTTTGAGATAATTTTAAATAATTTTTTTGTTGAAATGTGAATTGAAGACTCACAGTAATGCTGTTatct                                                                                             >  5:239144/1‑139 (MQ=255)
                                             cgcAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGTACTGAGAATTCCCGCCTCACATTCATGCTTTtctcg                                                                                             >  5:204675/1‑138 (MQ=255)
                                               cAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTGTTTTCAGATTATGTAAAAGAATGTATTTGTTGAACTGAGGATTCACGCCTCACGTTAATGCTTTTCTCTGc                                                                                           >  1:48335/1‑139 (MQ=255)
                                               cAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTGGTTTAAGATAATTTTAAAAAATTTATTTTTTTTACTGAGAATTAAAGACTCACATTCATGCATTTCTCTgg                                                                                           >  2:292437/1‑138 (MQ=255)
                                                   cGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAAAGGAAAAGAATTTTTTTTTTGTACTGAGAATTCAAGTCTAACATTGAAGCTTTTTTCTGgact                                                                                        >  7:325969/1‑138 (MQ=255)
                                                     caaatccaatGAGCGAAAACCAAATATCAATTACGCGATTTATTGCCAAATAACGAGCCGTATTTTCATATAATGTAAAAGAATTTATTTGTTTAACTGACAATTCACGACTCACATTCATGCTTTTCTCTGcactcac                                                                                     <  8:421263/137‑1 (MQ=255)
                                                         tccaatGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGGTGTACTGAGAATTAACGCCTCACATTCATGGGTTTCTCTGCACTCACGGac                                                                                 >  1:48161/1‑139 (MQ=255)
                                                            aatGAGCCCAAAACAAATATCCATTACGCGCTTTATTGCCAAAAAACGAGCCGTCTTTTCAGATAATGTAAAAGATTGTATTTTTTCAACTGAGAATCCACGACTCACATTCATGCTTTTCTCTGCACTCACTGacaca                                                                              <  7:392375/139‑1 (MQ=255)
                                                                acccaaaaCAAAATATCCATTACGCGTTTTATTGCAAAATAACGCGCCGTATTTTAATATAATCTAAAAGAATTTTTTTGTTGAACTTATAATCCACGACTCACATTCATGCTTTTCTCTGCACTCACTGacacacac                                                                           <  6:326786/133‑1 (MQ=255)
                                                                aGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACAcc                                                                          >  7:254858/1‑139 (MQ=255)
                                                                       aCCAAATCACCATTACGCGCTTTATTGCAAAATAACGCGCCTTCTTTTAATATAATTTAAAAGATTGTTTTTGTTCAACTGACACTCCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGAt                                                                   <  2:344435/139‑1 (MQ=255)
                                                                            atatCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCGTTTCAGATAATGTAAAAGAATGTTTTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCCCTCACTGACACACACCTCACGAtttgtt                                                              >  5:99678/1‑139 (MQ=255)
                                                                               tCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCATATAATGTAAAAGAATGTATTTGTTGAACTCAGAATTCACGACTCACATAAATGCTTTTCTCTGCACTCACTGACACACACCACACGAattgtt                                                              >  3:421400/1‑136 (MQ=255)
                                                                                  aTTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTAACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACCAGTTGTTTGGGAt                                                        >  5:81232/1‑139 (MQ=255)
                                                                                   ttccgcgTTTTATTCCAAAATAACCCCCCGTCTTTTCATATAATCAAAAACATTTTTTTTGTTCAACTGAAAATCCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTggg                                                          <  3:269652/133‑1 (MQ=255)
                                                                                   ttACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATg                                                       >  2:55772/1‑139 (MQ=255)
                                                                                   ttACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACGCCCATTCATGCTTTTCTCTGCACTCACTGCCACACCCCTCACGATTTGTTTGGGATg                                                       >  5:84165/1‑139 (MQ=255)
                                                                                        cgcTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCCCGACTCACATTCATGCTTTTCTCTGCCCTCACTGACACACACCTCACGATTTGTTTGGGATGTTat                                                   >  6:403588/1‑138 (MQ=255)
                                                                                        cgattaaTTGCCAAATACCGAGCCTTCTTTTCATATAATGTAAAATATTTTATTTGTTTAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTatg                                                  <  6:84165/133‑1 (MQ=255)
                                                                                         gcTTTATTCCCAAATACCGCCCCGTCTTATCAGATAATGAAAACTAATTTATTTTTTCACCTGTCAATGCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTatga                                                 <  5:75180/139‑1 (MQ=255)
                                                                                         gcTTTATTCCCAAATAACGAGCCGTCTTTTCAGATAATGAAAAAGTATGTATTTGTTGAACTGATAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTatga                                                 <  6:68804/139‑1 (MQ=255)
                                                                                         gcTTTATTCCAAAATAACGAGCCTTATTTTCATATATTTAAAAATAATTTTTTTTTTGAACTTATAATCCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTa                                                    <  3:384805/136‑1 (MQ=255)
                                                                                         gcTTTATGGCCAAAAAACGAGCCGTCTTTTCAGATAATGTAAAACAATTTATTTGTTCAACTGACAATGCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTa                                                    <  4:403912/136‑1 (MQ=255)
                                                                                              tatcccAAATAACGAGCCGGATTTGAAGATAATGTAAAATAATTTTTTTGTTGACCTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGAc                                             <  6:427617/134‑1 (MQ=255)
                                                                                                     aaTAACGAGCCGTGTTTTAAGATAATTTAAAATAATTTATTTTTTGAACTGAGAATTAACGCCTCACATTAAATCTTTTCTCTGCACTCACTGACACACACCACACGATTTGTTTGGGATGTTTTGATTACCTATTCca                                     >  8:168088/1‑139 (MQ=255)
                                                                                                     aaTAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACGAACATTCATGCTTTTCTCTGCAATCACTGACACACACCTCACGATTTGTTTGGGATTTTTTGATGAACTATGCca                                     >  6:324959/1‑139 (MQ=255)
                                                                                                     aaTAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTAACGACTCACATTCATGCTTTTGTCTGCACTCACTGACACACCCCTCACGATTTGTTTGGGATGTTATGATTACCTATGccc                                     >  6:395923/1‑138 (MQ=255)
                                                                                                        aaCGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACTCACATTAATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGccc                                     >  3:403912/1‑135 (MQ=255)
                                                                                                        aaCGAGCCGTCGTTTCTGATAATGTTAAAGAATGTATTTGTTGAACAGAGAATTACCGACTCCCAGTCATGGTGTTCTATGCCCTCACAGACACCCACCGCACCAGTTGTTTTGGCTGTTTTGATGACCTAAGccc                                     >  4:324103/1‑135 (MQ=255)
                                                                                                               cttCTTTTCATAAAAAGAAAACTAATTTTTTTGTTGACCTCACAACACACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAg                           <  2:48335/137‑1 (MQ=255)
                                                                                                                      taataaaaTGTAAAAGAATGTATTTGTTTAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAg                        <  3:418598/129‑1 (MQ=255)
                                                                                                                      tCAGAAAACGAACAAAAATGAATTGGTTGAACTACAAATCCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGACg                     <  8:14058/138‑1 (MQ=255)
                                                                                                                                     taaTTTATTTGTTGAACTGTGAATCCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGACGGATGTTAATTGGATGt     <  8:174828/138‑1 (MQ=255)
                                                                                                                                        tGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGACGGATGTTAATTGGATGTaaa  >  5:335742/1‑139 (MQ=255)
                                                                                                                                        tGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGACGGATGTTAATTGGATGTaaa  >  8:142817/1‑139 (MQ=255)
                                                                                                                                        tGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTAAGATGACCTATGCcagt                                   >  1:108619/1‑106 (MQ=255)
                                                                                                                                        tGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTAAGATGACCTATGCcagt                                   <  2:108619/106‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                         
CGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGACGGATGTTAATTGGATGTAAA  >  CP006881/3476555‑3476829

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A