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 2,992,747 A→C E218D (GAA→GAC)  ygeH → putative transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,992,7470AC95.6% 236.7 / 1.7 68E218D (GAA→GAC) ygeHputative transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (1/2);  new base C (31/34);  total (32/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

ATAAACCAGAATAATGCAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGAACTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCAGGACCAAGGATAT  >  NC_000913/2992652‑2992843
                                                                                               |                                                                                                
aTAAACCAGAATAATGCAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTAc                                                                                              >  1:1122089/1‑100 (MQ=255)
 cttccgatcttaatGCAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACa                                                                                             <  2:253360/90‑1 (MQ=255)
 cttccgatcttaatGCAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACa                                                                                             <  2:252742/90‑1 (MQ=255)
    aCCAGAATAATGCAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACataa                                                                                          >  2:930085/1‑100 (MQ=255)
     ccAGAATAATGCAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGAACTACataat                                                                                         <  1:997073/100‑1 (MQ=255)
      cAGAATAATGCAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACataata                                                                                        <  2:106820/100‑1 (MQ=255)
       aGAATAATGCAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATAc                                                                                       >  1:806432/1‑100 (MQ=255)
          ataatGCAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATc                                                                                    <  1:1001281/100‑1 (MQ=255)
           taatGCAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACaagatcggaag                                                                                   >  1:252745/1‑90 (MQ=255)
           taatGCAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACaagatcggaag                                                                                   >  1:253363/1‑90 (MQ=255)
            aatGCAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATcac                                                                                  <  1:73253/100‑1 (MQ=255)
             atGCAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATcaca                                                                                 >  1:318260/1‑100 (MQ=255)
                cAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAAtt                                                                              <  2:318257/100‑1 (MQ=255)
                  gttaaCACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAAttt                                                                             <  2:202607/96‑1 (MQ=255)
                  gTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATtta                                                                            <  1:1196191/100‑1 (MQ=255)
                    gAACGCTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATttatt                                                                          <  1:615645/100‑1 (MQ=255)
                    gAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATttatt                                                                          >  2:377642/1‑100 (MQ=255)
                     aaCACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATttatta                                                                         <  2:244029/100‑1 (MQ=255)
                        acTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAg                                                                      <  2:144116/100‑1 (MQ=255)
                        acTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAg                                                                      <  2:145491/100‑1 (MQ=255)
                          tttATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGat                                                                    >  1:752367/1‑100 (MQ=255)
                           ttATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGata                                                                   >  1:167966/1‑100 (MQ=255)
                             ataCATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGataat                                                                 <  2:898256/100‑1 (MQ=255)
                              taCATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGataata                                                                >  2:352477/1‑100 (MQ=255)
                                 aTTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATcc                                                             <  1:1131351/100‑1 (MQ=255)
                                 aTTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATATCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAAGATc                                                              <  2:63681/99‑1 (MQ=255)
                                  ttGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCt                                                            <  1:970261/100‑1 (MQ=255)
                                    gAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGAACTACATAATACATCACAATTTATTATAGATAATATCCTTc                                                          <  1:36444/100‑1 (MQ=255)
                                     aGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCa                                                         >  2:448767/1‑100 (MQ=255)
                                     aGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCa                                                         >  2:620208/1‑100 (MQ=255)
                                      gTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCaa                                                        >  1:1164247/1‑100 (MQ=255)
                                        tGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAAc                                                      <  2:212099/100‑1 (MQ=255)
                                        tGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAAc                                                      <  1:803285/100‑1 (MQ=255)
                                         gATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACg                                                     <  2:1208485/100‑1 (MQ=255)
                                         gATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACg                                                     <  2:751720/100‑1 (MQ=255)
                                          aTCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACgg                                                    >  1:272488/1‑100 (MQ=255)
                                           tCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGt                                                   <  2:1009487/100‑1 (MQ=255)
                                           tCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGt                                                   >  2:1066782/1‑100 (MQ=255)
                                            cGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTa                                                  >  1:1009496/1‑100 (MQ=255)
                                             gACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTAc                                                 <  1:366244/100‑1 (MQ=255)
                                              aCGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACa                                                <  2:245748/100‑1 (MQ=255)
                                                 cTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACAtta                                             >  1:1171033/1‑98 (MQ=255)
                                                  tAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATaaa                                            <  1:353597/100‑1 (MQ=255)
                                                  tAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATaaa                                            >  1:201150/1‑100 (MQ=255)
                                                    aaaaCCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAAcc                                          <  2:1262796/100‑1 (MQ=255)
                                                      aaCCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAg                                        >  1:1232396/1‑100 (MQ=255)
                                                         cTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAAc                                     >  1:435116/1‑100 (MQ=255)
                                                          ttttCCTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACg                                    <  2:1232385/100‑1 (MQ=255)
                                                               cTCATCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTg                               >  1:1967/1‑100 (MQ=255)
                                                                tCATCGCCAGTAATCATCTCCCTGTTGATGACCTACGTAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGt                              <  1:915509/100‑1 (MQ=255)
                                                                  aTCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTaa                            <  1:947377/100‑1 (MQ=255)
                                                                  aTCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTaa                            >  1:377607/1‑100 (MQ=255)
                                                                  aTCGCCAGTAATCATCTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTaa                            <  1:424115/100‑1 (MQ=255)
                                                                              catcTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGc                <  2:706461/100‑1 (MQ=255)
                                                                               atcTCCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCa               <  1:378219/100‑1 (MQ=255)
                                                                               atcTCCCTGTTGATGAACTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCa               >  1:4892/1‑100 (MQ=255)
                                                                                 ctcCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCAgg             >  2:1137181/1‑100 (MQ=255)
                                                                                 ctcCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCAgg             >  1:281472/1‑100 (MQ=255)
                                                                                 ctcCCTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCAgg             >  1:666167/1‑100 (MQ=255)
                                                                                   cccTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCAGGAc           <  1:448771/100‑1 (MQ=255)
                                                                                   cccTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCAGGAc           <  1:620212/100‑1 (MQ=255)
                                                                                   cccTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCAGGAc           >  2:177515/1‑100 (MQ=255)
                                                                                   cccTGTTGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCAGGAc           >  2:73443/1‑100 (MQ=255)
                                                                                        ttGATGACCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCAGGACCAAgg      <  1:1215128/100‑1 (MQ=255)
                                                                                         tgatgaCCTACATAATACATCACCATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTCTAAGTTTAACTAAGCAGGCCCAAGGa     >  2:1050447/1‑100 (MQ=255)
                                                                                         tgatgaCCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCAGGACCAAGGa     >  1:289541/1‑100 (MQ=255)
                                                                                            tgaCCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCAGGACCAAGGatat  >  1:96341/1‑100 (MQ=255)
                                                                                            tgaCCTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCAGGACCAAGGatat  >  1:178026/1‑100 (MQ=255)
                                                                                               |                                                                                                
ATAAACCAGAATAATGCAGTGAACACTTTATACATTGAGTTGATCGACGCTAAAAACCTTTTCCTCATCGCCAGTAATCATCTCCCTGTTGATGAACTACATAATACATCACAATTTATTATAGATAATATCCTTCAAACGGTACATAAACCAGAACGATCTGTAAGATTAGCTAAGCAGGACCAAGGATAT  >  NC_000913/2992652‑2992843

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A