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 3,186,737 T→A 22.3% I378F (ATC→TTC)  U712_16400 ← 3‑ketoacyl‑CoA thiolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,186,7370TA22.3% 55.2 / 2.6 38I378F (ATC→TTC) U712_164003‑ketoacyl‑CoA thiolase
Reads supporting (aligned to +/- strand):  ref base T (19/8);  new base A (2/6);  total (23/15)
Fisher's exact test for biased strand distribution p-value = 3.86e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATACATTTGATCGTATGTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTCCGCCGCCGATACACATGGTCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGATGAGTGAGAGTGTAAGCTTTGTGCCCGTACAGCCAAGCGGGTGTCCAAGCGCGATTGCGCCCCCGTTGACATTCAC  >  CP006881/3186604‑3186863
                                                                                                                                        |                                                                                                                              
ataCATTTGATCGTATGTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTCCGCCGCCGATacac                                                                                                                            <  5:162464/138‑1 (MQ=255)
 taCATTTGATCGTATGTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTCCGCCGCCGATACACAt                                                                                                                          >  8:53327/1‑139 (MQ=255)
 taCATTTGATCGTATGTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTCCGCCGCCGATACACAt                                                                                                                          >  4:6765/1‑139 (MQ=255)
      ttGATCGTATGTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑TCATAATTAAAATA‑CACCGGCCGCTACCATTCCGCCGGCGAGACACATGGTCa                                                                                                                     >  7:291255/1‑139 (MQ=255)
       tGATCGTTTGTCACACCCTCTATTAAAAATCCGCCCCGTTTTTTTACGTCCCCCGCTTTTTTTCCCATTTGTTTT‑TCCCCATTTA‑CCAAAATTAAAAAC‑CCCCGGCCGCCCCCATGCCGCCGCCGATACACATGGCCa                                                                                                                     <  6:128379/138‑1 (MQ=255)
         aTCGTATGTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGGCATTTTTTTT‑TGCCCCTTTA‑GCATAATTAAAATA‑CACCGGCCGCGGACATTCCCCCGCCGATACACAAggggccga                                                                                                                  >  3:200007/1‑133 (MQ=255)
         aTCGTATGTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCCTTCCGCCGCCGATACCAATGGTCaagc                                                                                                                  >  7:342068/1‑136 (MQ=255)
         aTCGTATGTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTCCGCCGCCGATACACATGGTCACGa                                                                                                                  >  7:196867/1‑139 (MQ=255)
         aTCGTATGTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTCCGCCGCCGATACACATGGTCACGa                                                                                                                  >  5:165633/1‑139 (MQ=255)
         aTCGTATGTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCGTTA‑GCATAATTCAAATA‑CACCGGCCGCGCCCATTCCGCCGCCGAATCCCATGGTCACGa                                                                                                                  >  3:355152/1‑139 (MQ=255)
         aTCGTATGTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TACCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTACGCCCCCGATACACATTGTCACGa                                                                                                                  >  8:218250/1‑139 (MQ=255)
         aTCGTATGTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGACGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTCCGCCGCCGCTACACATGGTCACgc                                                                                                                  >  5:157831/1‑138 (MQ=255)
         aTCGTATCTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTCCGCCGCCGATACACATGGTCACGa                                                                                                                  >  7:129218/1‑139 (MQ=255)
              aTGTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTCCGCCGCCGATACACATGGTCACGACTcc                                                                                                              >  4:181603/1‑138 (MQ=255)
                       ccTCGATTAAAAATCCGCCGCCTTTTTGTACGTGAGCCGGTTTTTTTGGCATTTGTTTT‑TTCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCTTTACGCCGGCGATACACATGGGGACGCCTCCAAATTGCTCg                                                                                                    >  7:79466/1‑139 (MQ=255)
                       ccTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTCCGCCGCCGAAACACAAGGTCACGACTCCAAATTGCTCg                                                                                                    >  7:62833/1‑139 (MQ=255)
                       ccTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGATCCCAATCCGCCGCCGATACACAAGGTCCCGACAACAAATTGCTCg                                                                                                    >  4:68955/1‑139 (MQ=255)
                        cTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTCCGCCGCCGATACACATGGTCACGACTCCAAATTGCTCGt                                                                                                   >  6:159720/1‑139 (MQ=255)
                                  atgccgccgCTTTTTTGTTGGTCATCCTCTTTTTTTGCC‑TTTGTTTTATCCCATTTTC‑CAAAAATAAAAATC‑CTCCGGCGGCTCCATTTCCGCGCCATACAAACTTGGTCACGACTCCAAATTGCTCGTTTCTCCGttt                                                                                         <  8:339653/136‑1 (MQ=255)
                                            cTTTTTGAACGCCAGCCGCTTTTTTTCCCATTTTTTTT‑CCCCCCTTTA‑CAAAAATTCAAATA‑CCCCGGCCGCACCCATTCCCCCCCCTATACACATGGCCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATgg                                                                               <  6:165633/139‑1 (MQ=255)
                                                    cggcccgCCTCTTTTTTTGCAATTTTTTTT‑ACCCCCTTTA‑CCAAAATACAAAAA‑CCCCGCCCGCGCCCATCCCCCCGCCGAAACACAGGGTCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGAtgagtg                                                                        <  8:153704/132‑1 (MQ=255)
                                                    cggacAGCCGCTTTTTTTGCAATTTTTTTT‑CCCCCCTTTC‑GCAAAATACAAAAC‑CCCCGCCCGCCCCCATCCCGCCGCCCAAAAACATGGCCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGAtgagtga                                                                       <  8:129218/135‑1 (MQ=255)
                                                    ccgtacgCCTCTTTTTTTG‑CATTTTTTTT‑TCCCCCTTTT‑ACAAAATTAAAAAACCCCCGGCCGCTCCAATTCCGCCCCCTAAACACATGGCCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGAtgagtg                                                                        <  3:68955/132‑1 (MQ=255)
                                                    aCGTCAGCCGTTTTTTTTCCCATTTGTTTT‑TCCCCCTTTA‑GATAAATTAAATTA‑ACCCGGCTGCTCCAATGCCGCCGCCTATAAACTTGGTCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGAtgagtga                                                                       <  7:218250/139‑1 (MQ=255)
                                                     gtcccgCCGCTTTTTTT‑CCATTTTGTTT‑TCCCCCATTATTAAAAAATAAAAAC‑CCCCGCCCGCCCCAATCCCGCCGCGGAACCACTGGGCCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGAtgagtgag                                                                      <  8:196867/134‑1 (MQ=255)
                                                     cGTCCGCCGTTTTTTTTGCAATTTGTTTT‑TCCCCCTTTA‑CAATAATTCAAAAC‑CCCCGCCCGCTCCCATTCCGCCGCCGATACACTTGGGCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGAtgagtga                                                                       <  2:247633/138‑1 (MQ=255)
                                                        cAGCCGCTTTTTTTGACATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTACGCCGCCGATACACATGGTCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGATGAGTGAGAgt                                                                   >  7:236012/1‑139 (MQ=255)
                                                                 tttttGCAATTTTTATT‑GCCCCATTTC‑GAAAAATAAAAAAA‑CCCCGCCCGCACCCATCCCCCCGCCTATACAATTGGCCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGATGAGTGAGAGTGTAAGCtt                                                           <  4:200007/138‑1 (MQ=255)
                                                                      gCCATTTCTTTT‑TCCCCCTTAA‑CATTAATACAAATA‑CACCGGCGGCCCCCTTCCCCCCCCCTATACCCATGGGCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGATGAGTGAGAGTGTAAGCTTTGTGc                                                      <  4:355152/138‑1 (MQ=255)
                                                                           ttGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTCCGCCGCCGATACACATGGTCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGATGAGTGAGAGTGTAAGCTTTTTGCCCGTa                                                 >  4:102017/1‑138 (MQ=255)
                                                                            tGTTTT‑TCCCCCTTTC‑GAATAATTAAAATC‑CCCCGGCCGCTCCAATTCCGCCGCCGAAACCCTGGGTCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGATGAGTGAGAGTGTAAGCTTTGTGCCCGTAc                                                <  7:364110/138‑1 (MQ=255)
                                                                            tGTTTT‑TCCCCATTTA‑CCATAATAAAAATA‑CCCCGGCCGCCCCCATCCCGCCGCCGAAACACATGGGCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGATGAGTGAGAGTGTAAGCTTTGTGCCCGTAc                                                <  5:159720/138‑1 (MQ=255)
                                                                                                    ttCAAATA‑CACCGGCCGCTCCCATTCCGCCGCCGAGACACAGGGTCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGATGAGTGAGAGTGTAAGCTTTGTGCCCGTACAGCCAAGCGGGTGTCCAAGcgcg                         >  5:290408/1‑139 (MQ=255)
                                                                                                         aTA‑CACCGGCCGCTCCCATTCCGCCGCCGATACACATGGTCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGATGAGTGAGAGTGTAAGCTTTGTGCCCGTACAGCCAAGCGGGTGTCCAAGCGCGATTgc                    >  2:234780/1‑139 (MQ=255)
                                                                                                                cGGCCGCTACCATTCCGCCGCCGATACACATGGTCACGACTCCAAATTGCACGTTTCTCCGTTTCAGTTCATGGATTAGTGAGAGGGTAAGCTTTTTGCCCCTACAGACAAGAGGGTGTCAAAGCGCGAATGCGccccc              >  6:303985/1‑139 (MQ=255)
                                                                                                                            ttCCGCCGCCGATACACATGGTCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGATGAGTGAGAGTGTAAGCTTTGTGCCCGTACAGCCAAGCGGGTGTCCAAGCGCGATTGCGCCCCCGGTGCCATTCAc  >  4:241498/1‑139 (MQ=255)
                                                                                                                            ctCCGCCGCCGATACACATGGTCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGATGAGTGAGAGTGTAAGCTTTGTGCCCGTAc                                                <  5:251846/92‑1 (MQ=255)
                                                                                                                            ctCCGCCGCCGATACACATGGTCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGATGAGTGAGAGTGTAAGCTTTGTGCCCGTAc                                                >  6:251846/2‑93 (MQ=255)
                                                                                                                                        |                                                                                                                              
ATACATTTGATCGTATGTGACATCCTCGATTAAAAATCCGCCGCCTTTTTGTACGTCAGCCGCTTTTTTTGCCATTTGTTTT‑TCCCCCTTTA‑GCATAATTCAAATA‑CACCGGCCGCTCCCATTCCGCCGCCGATACACATGGTCACGACTCCAAATTGCTCGTTTCTCCGTTTCATTTCATGGATGAGTGAGAGTGTAAGCTTTGTGCCCGTACAGCCAAGCGGGTGTCCAAGCGCGATTGCGCCCCCGTTGACATTCAC  >  CP006881/3186604‑3186863

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