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
A12 F56 I1 R1 165 53.8 2611523 96.4% 2517508 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,759,497 T→C C171C (TGT→TGC)  yfjI → CP4‑57 prophage; uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,759,4970TC98.3% 198.4 / ‑4.2 59C171C (TGT→TGC) yfjICP4‑57 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (28/30);  total (29/30)
Fisher's exact test for biased strand distribution p-value = 4.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.92e-01

GACTTAAAGAACTACTTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGTGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTACACACTTAACGAGCTGCCGTTTATCAATAAGA  >  NC_000913/2759400‑2759588
                                                                                                 |                                                                                           
gACTTAAAGAACTACTTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCgg                                                                                           <  1:102692/100‑1 (MQ=255)
 aCTTAAAGAACTACTTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCggg                                                                                          <  2:17215/100‑1 (MQ=255)
 aCTTAAAGAACTACTTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCggg                                                                                          <  1:649398/100‑1 (MQ=255)
  cTTAAAGAACTACTTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGc                                                                                         >  2:474002/1‑100 (MQ=255)
    tAAAGAACTACTTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCa                                                                                        <  1:474006/99‑1 (MQ=255)
    tAAAGAACTACTTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCAc                                                                                       >  2:595167/1‑100 (MQ=255)
    tAAAGAACTACTTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCAc                                                                                       >  2:658080/1‑100 (MQ=255)
      aaGAACTACTTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTg                                                                                     >  1:950448/1‑100 (MQ=255)
        gAACTACTTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGc                                                                                   <  2:115688/100‑1 (MQ=255)
        gAACTACTTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGc                                                                                   <  2:115850/100‑1 (MQ=255)
         aaCTACTTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCg                                                                                  >  1:332545/1‑100 (MQ=255)
          acttctTATGACAAACCAGAAAGCTCCAGTGATGTTCAAATTTTTATTTAATGATTTCACTCCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGa                                                                                 >  2:674785/1‑100 (MQ=255)
          actactTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGa                                                                                 <  2:8832/100‑1 (MQ=255)
           ctactTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGAt                                                                                <  1:1271861/100‑1 (MQ=255)
            tactTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATc                                                                               <  1:1198847/100‑1 (MQ=255)
            tactTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATc                                                                               <  1:696913/100‑1 (MQ=255)
             actTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCa                                                                              >  1:28968/1‑100 (MQ=255)
              ctTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAg                                                                             >  2:763067/1‑100 (MQ=255)
              ctTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAg                                                                             >  1:423727/1‑100 (MQ=255)
                    aCAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGca                                                                       >  2:675400/1‑100 (MQ=255)
                     cAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGcat                                                                      >  2:1282931/1‑100 (MQ=255)
                      aaaCCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGcatc                                                                     <  2:192406/100‑1 (MQ=255)
                      aaaCCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGcatc                                                                     <  2:850152/100‑1 (MQ=255)
                       aaCCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGcatca                                                                    <  1:1046369/100‑1 (MQ=255)
                       aaCCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGcatca                                                                    <  1:1122357/100‑1 (MQ=255)
                           cGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTc                                                                >  2:783995/1‑100 (MQ=255)
                               aGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCtgat                                                            <  1:287734/100‑1 (MQ=255)
                                 cTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCtgatga                                                          >  2:22467/1‑100 (MQ=255)
                                  tCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGaa                                                         >  2:195470/1‑100 (MQ=255)
                                   ccAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAg                                                        <  1:142395/100‑1 (MQ=255)
                                    cAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGc                                                       <  2:312546/100‑1 (MQ=255)
                                     aGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCt                                                      >  1:276604/1‑100 (MQ=255)
                                      gTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTACAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAGGCTg                                                     >  2:1053175/1‑100 (MQ=255)
                                       tGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTgg                                                    <  1:1300104/100‑1 (MQ=255)
                                        gagaTTCAAATTTTTATTTAACGATGCCACGCCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTggg                                                   <  2:177425/100‑1 (MQ=255)
                                        gagaTTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTggg                                                   >  2:1002069/1‑100 (MQ=255)
                                         agaTTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGa                                                  <  1:518911/100‑1 (MQ=255)
                                            ttCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCa                                               >  1:1195902/1‑100 (MQ=255)
                                              cAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCAtt                                             >  1:366294/1‑100 (MQ=255)
                                                aaTTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCAtttt                                           >  1:200729/1‑100 (MQ=255)
                                                 aTTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCAttttt                                          <  1:824684/100‑1 (MQ=255)
                                                    tttatttaACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAAt                                       <  2:282907/100‑1 (MQ=255)
                                                     ttatttaACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATg                                      <  2:895036/100‑1 (MQ=255)
                                                      tatttaACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATgg                                     >  1:999362/1‑100 (MQ=255)
                                                        tttaACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGtt                                   <  1:81772/100‑1 (MQ=255)
                                                         ttaACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTa                                  <  1:652521/100‑1 (MQ=255)
                                                         ttaACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTa                                  <  1:1002078/100‑1 (MQ=255)
                                                          taACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTac                                 <  2:366291/100‑1 (MQ=255)
                                                            aCGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAATCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTacac                               <  1:758710/100‑1 (MQ=255)
                                                             cGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTgcaca                              >  2:525934/1‑100 (MQ=255)
                                                                  ccACACCTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTACACACTTaa                         >  1:862390/1‑100 (MQ=255)
                                                                       ccTGCAGCTATTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTACACACTTAACGAGc                    >  1:1174889/1‑100 (MQ=255)
                                                                        cTGCAGCTATTATAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTACACACTTAACGAGCt                   <  1:551643/100‑1 (MQ=255)
                                                                         tGCAGCTATTAAAGCTCATCTCTGTGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTACACACTTAACGAGCTg                  >  1:717912/1‑100 (MQ=255)
                                                                                aTTAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTACACACTTAACGAGCTGCCGTTTa           >  1:957697/1‑100 (MQ=255)
                                                                                 ttAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTACACACTTAACGAGCTGCCGTTTAt          >  2:510824/1‑100 (MQ=255)
                                                                                  tAAAGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTACACACTTAACGAGCTGCCGTTTATc         <  1:212356/100‑1 (MQ=255)
                                                                                     aGCTCATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTACACACTTAACGAGCTGCCGTTTATCAAt      >  1:1288968/1‑100 (MQ=255)
                                                                                         cATCTCTGCGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTACACACTTAACGAGCTGCCGTTTATCAATAAGa  >  2:610772/1‑100 (MQ=255)
                                                                                                 |                                                                                           
GACTTAAAGAACTACTTACGACAAACCCGAAAGCTCCAGTGAGATTCAAATTTTTATTTAACGATGCCACACCTGCAGCTATTAAAGCTCATCTCTGTGGGCACTGGCGATCAGTCGGCATCATGTCTGATGAAGCTGGGATCATTTTTAATGGTTACACACTTAACGAGCTGCCGTTTATCAATAAGA  >  NC_000913/2759400‑2759588

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A