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
A11 F58 I0 R3 223 82.2 2922920 95.2% 2782619 126.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 2,631,395 G→T 39.1% Q402H (CAG→CAT)  U712_13545 → putative AAA domain‑containing protein YrvN

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068812,631,3950GT39.1% 42.7 / 58.6 51Q402H (CAG→CAT) U712_13545putative AAA domain‑containing protein YrvN
Reads supporting (aligned to +/- strand):  ref base G (18/13);  new base T (14/6);  total (32/19)
Fisher's exact test for biased strand distribution p-value = 5.54e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.49e-01

TAAAGGAGCTCAGGAATTAGGAAGAGGAATCGACTATAAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGTTTTTATGCATTATTTATCCTTCACACGTTTGATTTCAATGTC  >  CP006881/2631269‑2631529
                                                                                                                              |                                                                                                                                      
taAAGGAGCTCAGGAATTAGGAAGAGGAATCGACTATAAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACATCCCTGATCATCTGAAAAATAAGCAATACTATAAGCCGAAACATACTGGAAAGTTc                                                                                                                            >  3:50643/1‑139 (MQ=255)
     gAGCTCAGGAATTAGGAAGAGGAATCGACTATAAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATc                                                                                                                       <  3:62763/139‑1 (MQ=255)
      aGCTCAGGAATTAGGAAGAGGAATCGACTATAAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCt                                                                                                                      >  6:219975/1‑139 (MQ=255)
        cTCAGGAATTAGGAAGAGGAATCGACTATAAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAAt                                                                                                                        >  6:278537/1‑135 (MQ=255)
        cTCAGGAATTAGGAAGAGGAATCGACTATAAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAAt                                                                                                                        <  5:278537/135‑1 (MQ=255)
        cTCAGGAATTAGGAAGAGGAATCGACTATAAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGc                                                                                                                    >  8:136568/1‑139 (MQ=255)
        cTCAGGAATTAGGAAGAGGAATCGACTATAAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGc                                                                                                                    >  3:129868/1‑139 (MQ=255)
        cTCAGGAATTAGGAAGAGGAATCGACTATAAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTAGAAGCCGAAACAGACTGGAAAGTTCGAATCTGc                                                                                                                    >  3:83224/1‑139 (MQ=255)
                ttAGGAAGAGGAATCGACTATAAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGc                                                                                                            <  7:136568/139‑1 (MQ=255)
                ttAGGAAGAGGAATCGACTATAAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGc                                                                                                            <  5:112192/139‑1 (MQ=255)
                       gagGAATCGACTATAAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACATACTGGAAAGTTCGAAt                                                                                                                        <  1:362923/120‑1 (MQ=255)
                       gagGAATCGACTATAAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACATACTGGAAAGTTCGAAt                                                                                                                        >  2:362923/1‑120 (MQ=255)
                                  tataAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATc                                                                                                                       <  8:228369/110‑1 (MQ=255)
                                  tataAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATc                                                                                                                       >  7:228369/1‑110 (MQ=255)
                                    taAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAAt                                                                                         >  1:104962/1‑138 (MQ=255)
                                         aCCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACATACTGGAAAGTTCGAATc                                                                                                                       >  4:210376/1‑103 (MQ=255)
                                         aCCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACATACTGGAAAGTTCGAATc                                                                                                                       <  3:210376/103‑1 (MQ=255)
                                           ccGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATgaaaaga                                                                                  >  5:75678/1‑138 (MQ=255)
                                              cacaATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATACGCCGAAACAGACTGGAAAGATCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATgaaaagaaaa                                                                               >  4:180590/1‑138 (MQ=255)
                                              cacaATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAg                                                                                                             >  5:278452/1‑108 (MQ=255)
                                              cacaATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAg                                                                                                             <  6:278452/108‑1 (MQ=255)
                                                   ttACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATc                                                                                                                       <  1:161378/93‑1 (MQ=255)
                                                   ttACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATc                                                                                                                       >  2:161378/1‑93 (MQ=255)
                                                         cAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACATACTGGAAAGTTCGAATCTGCCTTAAAGCAg                                                                                                          <  4:111564/100‑1 (MQ=255)
                                                         cAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACATACTGGAAAGTTCGAATCTGCCTTAAAGCAg                                                                                                          >  3:111564/1‑100 (MQ=255)
                                                                 gggTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCATAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCtt                                                           >  2:272225/1‑139 (MQ=255)
                                                                            caaTACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAAGAGCCTTGATCCTCAAgg                                                <  1:272225/139‑1 (MQ=255)
                                                                             aaTACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGc                                               <  5:219975/139‑1 (MQ=255)
                                                                                  cTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACATACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCACGGCTCttt                                          >  1:97849/1‑139 (MQ=255)
                                                                                    cccTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACATACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGtttt                                         >  2:50626/1‑138 (MQ=255)
                                                                                    cccTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGc                                               <  4:147189/132‑1 (MQ=255)
                                                                                    cccTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGc                                               >  3:147189/1‑132 (MQ=255)
                                                                                    cccTGATCCTCTGAAAAATAAGAAATACTATAAGCCGAAACATACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGtttt                                         >  6:114394/1‑138 (MQ=255)
                                                                                    cacTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACATACTGGAAAGTTAGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGatta                                         >  8:7908/3‑137 (MQ=255)
                                                                                     ccTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTCGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGTTTTTa                                       <  3:139151/139‑1 (MQ=255)
                                                                                         aTCCTCTGAAAAATAAGCAATACTATAACCCGAAACATACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGTTTTTATGCa                                   <  3:318904/139‑1 (MQ=255)
                                                                                              ctGAAAAATAAGCAATACTATAAGCCGAAACATACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTg                                                          >  3:116683/1‑111 (MQ=255)
                                                                                              ctGAAAAATAAGCAATACTATAAGCCGAAACATACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTg                                                          <  4:116683/111‑1 (MQ=255)
                                                                                               tGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGTTTTTATGCattatt                              <  2:104962/138‑1 (MQ=255)
                                                                                                              aCTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGTTTTTATGCATTATTTATCCTTCACACGttt              >  3:186824/1‑139 (MQ=255)
                                                                                                                  taAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGACAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGTTTTTATGCAttattta                            <  1:182179/121‑1 (MQ=255)
                                                                                                                  taAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGTTTTTATGCAttattta                            >  2:182179/1‑121 (MQ=255)
                                                                                                                    aGCCGAAACATACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGTTTTTATGCATTATTTATCCTTCACACGTTTGAttt         >  3:191398/1‑138 (MQ=255)
                                                                                                                       cGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGCCTGTTTTTATGCAGTATTTATCCTTCACACGTTTGATTTCAAt     >  8:131672/1‑139 (MQ=255)
                                                                                                                          aaCATACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGc                                               <  4:164121/94‑1 (MQ=255)
                                                                                                                          aaCATACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGc                                               >  3:164121/1‑94 (MQ=255)
                                                                                                                          aaCATACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGTTTTTATGCATTATTTATCCTTCACACGTTTGATTTCAATGTc  >  2:340086/1‑139 (MQ=255)
                                                                                                                          aaCATACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGTTTTTATGCATTATTTATCCTTCACACGTTTGATTTCAATGTc  >  4:148087/1‑139 (MQ=255)
                                                                                                                          aaCATACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGTTTTTATGCATTATTTATCCTTCACACGTTTGATTTCAATGTc  >  8:271843/1‑139 (MQ=255)
                                                                                                                          aaCAGACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGTTTTTATGCATTATTTATCCTTCACACGTTTGATTTCAATGTc  >  5:82988/1‑139 (MQ=255)
                                                                                                                          aaCAGACTGGAAAGTTCGAATCTGCCATAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGTTTTTATGCATTATTTATCCTTCACACGTTTGATTTCAATGTc  >  5:203845/1‑139 (MQ=255)
                                                                                                                              |                                                                                                                                      
TAAAGGAGCTCAGGAATTAGGAAGAGGAATCGACTATAAATACCCGCACAATTACGACAACGGTTGGGTCGAACAACAATACCTCCCTGATCCTCTGAAAAATAAGCAATACTATAAGCCGAAACAGACTGGAAAGTTCGAATCTGCCTTAAAGCAGGTGTACGATAAATTAATGAAAAGAAAATAAAACAAAAAAACAGCCTTGATCATCAAGGCTGTTTTTATGCATTATTTATCCTTCACACGTTTGATTTCAATGTC  >  CP006881/2631269‑2631529

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