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 3,727,880 T→C intergenic (‑132/+37) yiaB ← / ← xylB YiaAB family inner membrane protein/xylulokinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,727,8800TC96.6% 191.0 / ‑4.0 59intergenic (‑132/+37)yiaB/xylBYiaAB family inner membrane protein/xylulokinase
Reads supporting (aligned to +/- strand):  ref base T (0/2);  new base C (29/28);  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 = 1.00e+00

CCAACGAAAGACAAAACTGAAAAATGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGTGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGAACGTTTCTCGTCGTGGCTG  >  NC_000913/3727787‑3727976
                                                                                             |                                                                                                
ccAACGAAAGACAAAACTGAAAAATGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTa                                                                                            >  2:295853/1‑100 (MQ=255)
ccAACGAAAGACAAAACTGAAAAATGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTa                                                                                            <  1:411207/100‑1 (MQ=255)
 cAACGAAAGACAAAACTGAACAATGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTAt                                                                                           >  2:795972/1‑100 (MQ=255)
 cAACGAAAGACAAAACTGAAAAATGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTAt                                                                                           >  2:442435/1‑100 (MQ=255)
  aaCGAAAGACAAAACTGTAAAATGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATc                                                                                          >  2:452928/1‑100 (MQ=255)
        aGACAAAACTGAAAAATGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCAc                                                                                    >  2:624102/1‑100 (MQ=255)
            aaaaCTGAAAAATGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCgg                                                                                <  2:140598/100‑1 (MQ=255)
                cTGAAAAATGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTcag                                                                            >  1:373861/1‑100 (MQ=255)
                cTGAAAAATGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTca                                                                             >  1:529239/1‑99 (MQ=255)
                cTGAAAAATGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATACCCTACCCGGTca                                                                             >  2:865769/1‑99 (MQ=255)
                cTGAAAAATGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATACCCCACCCg                                                                                 >  2:15907/1‑95 (MQ=255)
                  gAAAAATGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTcaggc                                                                          >  1:258626/1‑100 (MQ=255)
                     aaaTGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCTAATTATCCCCCACCCGGTcaggcagg                                                                       <  2:171/100‑1 (MQ=255)
                          ccATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATa                                                                  <  1:1192074/100‑1 (MQ=255)
                               aaCAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGtt                                                             <  1:442439/100‑1 (MQ=255)
                                aCAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGttt                                                            >  2:535450/1‑100 (MQ=255)
                                 cAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTa                                                           >  2:757930/1‑100 (MQ=255)
                                 cAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTa                                                           >  1:817429/1‑100 (MQ=255)
                                  aaaTGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTAc                                                          <  2:840508/100‑1 (MQ=255)
                                  aaaTGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATACCCCACCCGGTCAGGCAGGGGATAACGTTTAc                                                          >  2:490387/1‑100 (MQ=255)
                                   aaTGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACg                                                         <  1:963320/100‑1 (MQ=255)
                                   aaTGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACg                                                         <  2:948833/100‑1 (MQ=255)
                                       aTTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGCGATAACGTTTACGCCa                                                      >  1:567958/1‑99 (MQ=255)
                                       aTTTTCAGAATAAATTCATACTAAATATTAATTAATTAATGAGATATATAGATGCGAATTATCCTCAACACGGTCAGGCAGGGGATAACGTTTACGCCAt                                                     >  2:823506/1‑100 (MQ=255)
                                         tttCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTa                                                   <  2:1166022/100‑1 (MQ=255)
                                         tttCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTa                                                   <  1:1100626/100‑1 (MQ=255)
                                              gAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGc                                              <  1:448546/100‑1 (MQ=255)
                                              gAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGc                                              <  1:743980/100‑1 (MQ=255)
                                                 tAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGa                                           >  2:678710/1‑100 (MQ=255)
                                                 tAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGa                                           <  2:813131/100‑1 (MQ=255)
                                                   aaTTCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAg                                         >  1:44851/1‑100 (MQ=255)
                                                      tCATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTg                                      <  2:649865/100‑1 (MQ=255)
                                                       cATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGc                                     <  2:954029/100‑1 (MQ=255)
                                                       cATACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGc                                     >  1:813751/1‑100 (MQ=255)
                                                        aTACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCt                                    <  2:679515/100‑1 (MQ=255)
                                                         tACTAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTg                                   <  1:63063/100‑1 (MQ=255)
                                                            tAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATa                                <  1:452932/100‑1 (MQ=255)
                                                            tAAATATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATa                                <  2:197727/100‑1 (MQ=255)
                                                             aaaTATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATag                               <  2:265973/100‑1 (MQ=255)
                                                             aaaTATTAATTAATTACTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATag                               <  2:957138/100‑1 (MQ=255)
                                                                 attaattaattaCTGAGATATATAGATGTGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGc                           <  2:1285451/100‑1 (MQ=255)
                                                                 attaattaattaCTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGc                           <  1:889882/100‑1 (MQ=255)
                                                                    aattaattaCTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGAc                        >  1:654017/1‑100 (MQ=255)
                                                                    aattaattaCTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGAc                        >  2:407862/1‑100 (MQ=255)
                                                                     attaattaCTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACg                       >  1:152568/1‑100 (MQ=255)
                                                                       taattaCTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGa                     >  2:507500/1‑100 (MQ=255)
                                                                        aattaCTGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGaa                    >  1:580448/1‑100 (MQ=255)
                                                                           taCTGAGATATATAGATGCGAATTATCCCCCTCCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGAACg                  <  1:239345/99‑1 (MQ=255)
                                                                              tGAGATATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGAACGTTtc              <  1:293419/100‑1 (MQ=255)
                                                                              tGAGATATATAGATGCGAATTAGCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGAACGtt                <  2:997083/98‑1 (MQ=255)
                                                                               gagaTATATAGATGTGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGAACGTTtct             <  1:107413/100‑1 (MQ=255)
                                                                               gagaTATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGAACGTTtc              >  2:1032689/1‑99 (MQ=255)
                                                                                agaTATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGAACGTTtctc            >  2:700951/1‑100 (MQ=255)
                                                                                 gaTATATAGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGAACGTTTCtcg           >  2:1142791/1‑100 (MQ=255)
                                                                                        aGATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGAACGTTTCTCGTCGTGGc    <  1:55381/100‑1 (MQ=255)
                                                                                         gATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGATGCGACGGAACGTTTCTCGTCGTGGCt   <  1:795977/100‑1 (MQ=255)
                                                                                         gATGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGAACGTTTCTCGTCGTGGCt   >  2:1074038/1‑100 (MQ=255)
                                                                                          aTGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGAACGTTTCTCGTCGTGGCTg  >  1:487588/1‑100 (MQ=255)
                                                                                          aTGCGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGAACGTTTCTCGTCGTGGCTg  <  2:44850/100‑1 (MQ=255)
                                                                                             |                                                                                                
CCAACGAAAGACAAAACTGAAAAATGCCATTAACAAATGATTTTCAGAATAAATTCATACTAAATATTAATTAATTACTGAGATATATAGATGTGAATTATCCCCCACCCGGTCAGGCAGGGGATAACGTTTACGCCATTAATGGCAGAAGTTGCTGATAGAGGCGACGGAACGTTTCTCGTCGTGGCTG  >  NC_000913/3727787‑3727976

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A