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 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,001,511 T→C 12.8% I81T (ATA→ACA)  xdhB → xanthine dehydrogenase, FAD‑binding subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,001,5110TC12.8% 203.5 / 21.3 78I81T (ATA→ACA) xdhBxanthine dehydrogenase, FAD‑binding subunit
Reads supporting (aligned to +/- strand):  ref base T (35/33);  new base C (6/4);  total (41/37)
Fisher's exact test for biased strand distribution p-value = 7.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.10e-01

GGAATTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCGC  >  W3110S.gb/3001447‑3001579
                                                                |                                                                    
ggAATTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATagaaga                                                                <  1:2438259/71‑1 (MQ=255)
   aTTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATcc                                                             >  1:1203919/1‑71 (MQ=255)
   aTTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATcc                                                             >  1:3667450/1‑71 (MQ=255)
      aCGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCta                                                           >  1:62726/1‑70 (MQ=255)
       cGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCtat                                                          <  1:3632715/70‑1 (MQ=255)
        gCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATaga                                                                   <  1:2394586/60‑1 (MQ=255)
            gCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATagaag                                                                 >  1:2427013/1‑58 (MQ=255)
            gCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATaa                                                        >  1:43117/1‑67 (MQ=255)
            gCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACt                                                      <  1:940662/69‑1 (MQ=255)
            gCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACt                                                      <  1:1359690/69‑1 (MQ=255)
               gAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACg                                                 >  1:3542838/1‑71 (MQ=255)
               gAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACg                                                 >  1:2299828/1‑71 (MQ=255)
               gAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACg                                                 >  1:2000527/1‑71 (MQ=255)
                aaGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGt                                                >  1:3394307/1‑71 (MQ=255)
                aaGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGt                                                >  1:4104343/1‑71 (MQ=255)
                 aGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTc                                               <  1:4497874/71‑1 (MQ=255)
                   aTGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATaa                                                        >  1:2512103/1‑60 (MQ=255)
                   aTGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCa                                              >  1:2166692/1‑70 (MQ=255)
                    tGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCtat                                                          <  1:3699276/57‑1 (MQ=255)
                     ggCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATagaa                                                                  >  1:30018/1‑48 (MQ=255)
                      gCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAAc                                                       <  1:4594342/58‑1 (MQ=255)
                      gCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCAtctc                                          >  1:1661644/1‑71 (MQ=255)
                        tCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTccc                                        >  1:4421704/1‑71 (MQ=255)
                        tCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTccc                                        >  1:664464/1‑71 (MQ=255)
                         cGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCg                                       >  1:2354704/1‑71 (MQ=255)
                          gCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCa                                              >  1:3439831/1‑63 (MQ=255)
                          gCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCa                                              >  1:257541/1‑63 (MQ=255)
                          gCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCg                                       <  1:1926425/70‑1 (MQ=255)
                          gCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCg                                       >  1:4312536/1‑70 (MQ=255)
                              cGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCg                                    <  1:2035629/69‑1 (MQ=255)
                              cGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGt                                   >  1:2201008/1‑70 (MQ=255)
                              cGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGt                                   >  1:3878452/1‑70 (MQ=255)
                                tATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAt                                <  1:1648099/71‑1 (MQ=255)
                                  tCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACg                                                 <  1:323112/52‑1 (MQ=255)
                                    ggCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCg                                       >  1:2978364/1‑60 (MQ=255)
                                     gCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGtgct                           <  1:4271233/71‑1 (MQ=255)
                                      ctctGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGtgctg                          <  1:2487541/71‑1 (MQ=255)
                                       tctGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGtgctgc                         >  1:2766226/1‑71 (MQ=255)
                                         tGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGtgctgc                         <  1:2054249/69‑1 (MQ=255)
                                         tGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGtgctgc                         <  1:3710979/69‑1 (MQ=255)
                                         tGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGtgctg                          <  1:1411904/68‑1 (MQ=255)
                                           cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGtt                                  <  1:4435871/58‑1 (MQ=255)
                                           cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTa                                 <  1:890478/59‑1 (MQ=255)
                                           cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGc                      <  1:2463729/70‑1 (MQ=255)
                                           cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCATTATGTGCTGCGGc                      >  1:3999248/1‑70 (MQ=255)
                                            aaCGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCa                    >  1:3927343/1‑71 (MQ=255)
                                             aCGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCAc                   >  1:438985/1‑71 (MQ=255)
                                              cGACATTTAACCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACg                  <  1:1814874/71‑1 (MQ=255)
                                               gACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGt                 <  1:1059063/71‑1 (MQ=255)
                                                aCATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTc                >  1:1111358/1‑71 (MQ=255)
                                                 cATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTc                >  1:2019081/1‑70 (MQ=255)
                                                  aTTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCAtctc                                          <  1:3970944/43‑1 (MQ=255)
                                                  aTTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCa              >  1:3884713/1‑71 (MQ=255)
                                                   tttACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGtgctg                          <  1:3810932/58‑1 (MQ=255)
                                                   tttACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCAt             <  1:1024008/71‑1 (MQ=255)
                                                    ttACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCAtt            >  1:1274118/1‑71 (MQ=255)
                                                    ttACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCAtt            >  1:3243733/1‑71 (MQ=255)
                                                    ttACCCAGCTAACAGAAGATCCTATAACTCAACGTAATCTCCCGGCGTTATGTGCTGCGGCCACGTCCAtt            >  1:2319128/1‑71 (MQ=255)
                                                      aCCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTg           <  1:4204096/70‑1 (MQ=255)
                                                       cccAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGc          <  1:3558173/70‑1 (MQ=255)
                                                        ccAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCg                                    <  1:4427116/43‑1 (MQ=255)
                                                        ccAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTg        >  1:1448323/1‑71 (MQ=255)
                                                        ccAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTg        <  1:842646/71‑1 (MQ=255)
                                                        ccAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTg        >  1:3526534/1‑71 (MQ=255)
                                                          aGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGc                      >  1:3702078/1‑55 (MQ=255)
                                                          aGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGa      <  1:3520220/71‑1 (MQ=255)
                                                          aGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGa      >  1:4284851/1‑71 (MQ=255)
                                                           gCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGtt                                  <  1:3206921/42‑1 (MQ=255)
                                                            cTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGc          >  1:659761/1‑65 (MQ=255)
                                                            cTAATAGAAGATCCTATAACTCAACGTCATCTCCC‑GCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCg   <  1:2708059/71‑1 (MQ=255)
                                                             tAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGAcc    <  1:4306652/70‑1 (MQ=255)
                                                             tAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTg        >  1:2855867/1‑66 (MQ=255)
                                                              aaTAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGc                      <  1:4352437/51‑1 (MQ=255)
                                                              aaTAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGa      >  1:3512553/1‑67 (MQ=255)
                                                              aaTAGAAGATCCTATAACTCAACGTAATCTCCCGGCGtt                                  >  1:4001024/1‑39 (MQ=255)
                                                               aTAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCg   <  1:1647177/69‑1 (MQ=255)
                                                               aTAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCg   <  1:1356029/69‑1 (MQ=255)
                                                               aTAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCGc  <  1:3300609/70‑1 (MQ=255)
                                                                |                                                                    
GGAATTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCGC  >  W3110S.gb/3001447‑3001579

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A