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
A5 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 1,088,483 C→T 44.3% Q599Q (CAG→CAA)  ycdR ← predicted enzyme associated with biofilm formation

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,088,4830CT44.3% 23.7 / 79.1 61Q599Q (CAG→CAA) ycdRpredicted enzyme associated with biofilm formation
Reads supporting (aligned to +/- strand):  ref base C (17/17);  new base T (13/14);  total (30/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.01e-01

CCTGATGCTGACCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGCCGATTTTTCTGCGA  >  W3110S.gb/1088419‑1088547
                                                                |                                                                
ccTGATGCTGACCATTTTTCTGCCAGTTTTGTGCCTTTAATTCTAAAATAGATTTGTCTTTAGCTTGAggg                                                            <  1:1339295/71‑1 (MQ=255)
   gATGCTGACCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATg                                                         >  1:2808496/1‑71 (MQ=255)
    aTGCTGACCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGAt                                                          <  1:4604850/69‑1 (MQ=255)
    aTGCTGACCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATg                                                         <  1:4335024/70‑1 (MQ=255)
     tGCTGACCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGt                                                        <  1:3003649/70‑1 (MQ=255)
       cTGACCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGtttt                                                     <  1:2801938/71‑1 (MQ=255)
       cTGACCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGtttt                                                     <  1:4822528/71‑1 (MQ=255)
          aCCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTa                                                   <  1:4721367/70‑1 (MQ=255)
          aCCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTaa                                                  >  1:1713490/1‑71 (MQ=255)
            cATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATtttttt                                                    <  1:4179681/67‑1 (MQ=255)
            cATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAAtt                                                >  1:3502611/1‑71 (MQ=255)
             aTTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGttttt                                                    <  1:3330737/66‑1 (MQ=255)
             aTTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGttttt                                                    <  1:1914093/66‑1 (MQ=255)
              tttttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTaa                                                  >  1:1913506/1‑67 (MQ=255)
               ttttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGa                                             >  1:4363527/1‑71 (MQ=255)
               ttttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGa                                             >  1:2341205/1‑71 (MQ=255)
                  tCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGAtt                                           <  1:3599135/70‑1 (MQ=255)
                      acAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTa                                                   <  1:2896756/57‑1 (MQ=255)
                          ttttGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTg                                  <  1:3005049/71‑1 (MQ=255)
                            ttGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAAt                                                 >  1:1489273/1‑54 (MQ=255)
                            ttGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGGTTTTAATTTGATTGGTCAATTGTa                                >  1:965191/1‑71 (MQ=255)
                               tgCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGAt                                            <  1:2944339/56‑1 (MQ=255)
                               tgCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGAt                                            <  1:1432342/56‑1 (MQ=255)
                                gCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTg                                          >  1:83829/1‑57 (MQ=255)
                                gCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTg                                          >  1:2726742/1‑57 (MQ=255)
                                gCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTAtt                              <  1:1571308/69‑1 (MQ=255)
                                  cTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAAcc                          <  1:4682340/71‑1 (MQ=255)
                                   tGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGtttt                                                     <  1:4707451/43‑1 (MQ=255)
                                   tGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCa                         >  1:3474353/1‑71 (MQ=255)
                                     tAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGa                                             >  1:775105/1‑49 (MQ=255)
                                     tAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAAtt                                   >  1:2534733/1‑59 (MQ=255)
                                     tAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCAt                        <  1:2566920/70‑1 (MQ=255)
                                     tAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATCTGa                                             >  1:164939/1‑49 (MQ=39)
                                      aaTTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGAt                                            >  1:181658/1‑49 (MQ=255)
                                      aaTTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTg                      >  1:3993519/1‑71 (MQ=255)
                                       aTTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTgg                     <  1:4491350/71‑1 (MQ=255)
                                       aTTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTgg                     <  1:4999427/71‑1 (MQ=255)
                                        ttCTAAAATAGATTTCTCTTTAGCTTGAGGGATGTTTTTAAttt                                               <  1:3410448/44‑1 (MQ=38)
                                         tCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGa                                             >  1:3217450/1‑45 (MQ=255)
                                         tCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGa                                             >  1:310513/1‑45 (MQ=255)
                                          cTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGt                    >  1:1148467/1‑69 (MQ=255)
                                             aaaTAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGcc               >  1:1867496/1‑71 (MQ=255)
                                               aTAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGCCGa             <  1:877552/71‑1 (MQ=255)
                                                tAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGa                                             >  1:4066750/1‑38 (MQ=255)
                                                tAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGa                                             >  1:1723836/1‑38 (MQ=255)
                                                tAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGa                                             >  1:4080132/1‑38 (MQ=255)
                                                 aGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCa                         >  1:815516/1‑57 (MQ=255)
                                                  gATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGCCGAtt           <  1:715128/70‑1 (MQ=255)
                                                    tttGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGCCGAttttt        <  1:1419606/71‑1 (MQ=255)
                                                     ttGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGCCGATTTTTc       >  1:2720957/1‑71 (MQ=255)
                                                      tGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGCCGATTTTTc       <  1:1147219/70‑1 (MQ=255)
                                                       gTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTa                                >  1:3237334/1‑44 (MQ=255)
                                                       gTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTGAATTGTATTAACCATTGGTCAGcc               >  1:1573594/1‑61 (MQ=255)
                                                       gTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGcc               >  1:3489918/1‑61 (MQ=255)
                                                       gTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGcc               >  1:4406842/1‑61 (MQ=255)
                                                        tCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTg                                  <  1:331446/41‑1 (MQ=255)
                                                        tCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTg                                  <  1:4194618/41‑1 (MQ=255)
                                                        tCTTTAGCTTGAGGGATG‑TTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGCCGATTTTTCTGc    <  1:1234830/70‑1 (MQ=255)
                                                          tttAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTgg                     <  1:2102152/52‑1 (MQ=255)
                                                          tttAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGt                    <  1:3510105/53‑1 (MQ=255)
                                                           ttAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGCCGATTTTTCTGCGa  >  1:4786694/1‑70 (MQ=255)
                                                                |                                                                
CCTGATGCTGACCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGCCGATTTTTCTGCGA  >  W3110S.gb/1088419‑1088547

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A