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
A2 F3 I0 R2 232 76.3 4135488 90.9% 3759158 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,027,446 A→G 20.8% N134S (AAC→AGC)  malX → fused maltose and glucose‑specific PTS enzyme IIBC components

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,027,4460AG20.8% 212.7 / 53.1 101N134S (AAC→AGC) malXfused maltose and glucose‑specific PTS enzyme IIBC components
Reads supporting (aligned to +/- strand):  ref base A (46/34);  new base G (14/7);  total (60/41)
Fisher's exact test for biased strand distribution p-value = 6.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

Only 100 of 102 total aligned reads displayed.

GTAAACTTCTGGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTCGGTGCGGTGATCGCCGGTATTATC  >  minE/1027379‑1027516
                                                                   |                                                                      
gTAAACTTCTTGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACAt                                                                     <  1:2146784/71‑1 (MQ=255)
gTAAACTTCTGGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACAt                                                                     <  1:3500241/71‑1 (MQ=255)
gTAAACTTCTGGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACAt                                                                     <  1:2151589/71‑1 (MQ=255)
gTAAACTTCTGGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACAt                                                                     <  1:1768887/71‑1 (MQ=255)
 tAAGCTTCTGGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATc                                                                    >  1:1076485/1‑71 (MQ=255)
 tAAACTTCTGGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACAt                                                                     <  1:3734330/70‑1 (MQ=255)
     cTTCTGGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATc                                                                    >  1:2074653/1‑67 (MQ=255)
     cTTCTGGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCa                                                                  >  1:220155/1‑69 (MQ=255)
     cTTCTGGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCa                                                                  >  1:2863630/1‑69 (MQ=255)
        cTGGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAGCATCCagag                                                               <  1:375168/69‑1 (MQ=255)
        cTGGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAGCATCCAGAGCa                                                             >  1:3318627/1‑71 (MQ=255)
        cTGGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAGCATCCAGAGCa                                                             >  1:1893643/1‑71 (MQ=255)
        cTGGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCa                                                             >  1:3641825/1‑71 (MQ=255)
           gTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAGCATCCAGAGCa                                                             <  1:123633/68‑1 (MQ=255)
           gTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCAtt                                                           <  1:2080760/70‑1 (MQ=255)
            ttGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCt                                                         >  1:1066950/1‑71 (MQ=255)
            ttGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCt                                                         >  1:1821297/1‑71 (MQ=255)
              gACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCAtt                                                           >  1:1843799/1‑67 (MQ=255)
              gACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCAtt                                                           >  1:2119556/1‑67 (MQ=255)
              gACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCAtt                                                           >  1:1373222/1‑67 (MQ=255)
              gACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCAtt                                                           >  1:3590419/1‑67 (MQ=255)
              gACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAAAATCCAGAGCAtt                                                           >  1:2682606/1‑67 (MQ=255)
                   aTAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATc                                                  >  1:752795/1‑71 (MQ=255)
                    tAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTggg                                                     <  1:489758/67‑1 (MQ=255)
                    tAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTggg                                                     <  1:3466470/67‑1 (MQ=255)
                    tAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTggg                                                     <  1:3549622/67‑1 (MQ=255)
                     aaaGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATc                                                  >  1:1933741/1‑69 (MQ=255)
                      aaGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAGCATCCAGAGCATTCTTGGGATCCa                                                >  1:3286947/1‑70 (MQ=255)
                      aaGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAg                                               >  1:1994273/1‑71 (MQ=255)
                      aaGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAg                                               >  1:2605766/1‑71 (MQ=255)
                      aaGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAg                                               >  1:1065972/1‑71 (MQ=255)
                      aaGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAg                                               >  1:3830685/1‑71 (MQ=255)
                           aTTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCAtt                                                           <  1:327981/54‑1 (MQ=255)
                            ttCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAGCATCCAGAGCATTc                                                          <  1:2424142/54‑1 (MQ=255)
                            ttCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAGCATCCAGAGCATTc                                                          <  1:1300849/54‑1 (MQ=255)
                            ttCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCagag                                                               <  1:2677142/49‑1 (MQ=255)
                            ttCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCagag                                                               <  1:1726121/49‑1 (MQ=255)
                            ttCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGtcgatc                                         <  1:3975504/71‑1 (MQ=255)
                              cTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAAc                                                                       >  1:1965050/1‑39 (MQ=255)
                              cTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAAc                                                                       >  1:1431968/1‑39 (MQ=255)
                              cTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAAc                                                                       >  1:2517240/1‑39 (MQ=255)
                              cTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAAc                                                                       >  1:3913346/1‑39 (MQ=255)
                              cTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCaga                                                                >  1:308277/1‑46 (MQ=255)
                              cTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCaga                                                                >  1:2426152/1‑46 (MQ=255)
                              cTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCaga                                                                >  1:1770142/1‑46 (MQ=255)
                              cTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCaga                                                                >  1:4082340/1‑46 (MQ=255)
                              cTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCAtt                                                           >  1:1296096/1‑51 (MQ=255)
                              cTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGtcgatcga                                       >  1:1671289/1‑71 (MQ=255)
                              cTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGtcgatcg                                        >  1:381892/1‑70 (MQ=255)
                              cTGCAAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCAtt                                                           >  1:3093014/1‑51 (MQ=255)
                                   aaCCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCg                                  >  1:3848404/1‑71 (MQ=255)
                                   aaCCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCg                                  >  1:2701454/1‑71 (MQ=255)
                                   aaCCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCg                                  >  1:731095/1‑71 (MQ=255)
                                    aCCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTg                                                       <  1:2529009/49‑1 (MQ=255)
                                    aCCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTg                                                       <  1:2573156/49‑1 (MQ=255)
                                    aCCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTg                                                       <  1:1552304/49‑1 (MQ=255)
                                    aCCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTg                                                       <  1:2765221/49‑1 (MQ=255)
                                    aCCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGtcgatc                                         <  1:1520344/63‑1 (MQ=255)
                                    aCCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGtcgatc                                         <  1:2824325/63‑1 (MQ=255)
                                    aCCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGtcgatc                                         <  1:1697674/63‑1 (MQ=255)
                                    aCCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATAc                                    <  1:1939034/68‑1 (MQ=255)
                                    aCCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATAc                                    <  1:2769180/68‑1 (MQ=255)
                                      cACGGATTCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTgcg                                                     >  1:3486517/1‑47 (MQ=39)
                                      cACGGATGCCGCGGTTCTGAAAGCCAATAGCATCCAGAGCATTCTTGTGATCCAGTCGATCGATa                                     >  1:2998438/1‑65 (MQ=255)
                                      cACGGATGCCGCGGTTCTGAAAGCCAATAGCATCCAGAGCATTCTTGGGATCCAGTCGATCGATa                                     >  1:751445/1‑65 (MQ=255)
                                      cACGGATGCCGCGGTTCTGAAAGCCAATAGCATCCAGAGCATTCTTGGGATCCAGTCGATCGATa                                     >  1:3673246/1‑65 (MQ=255)
                                      cACGGATGCCGCGGTTCTGAAAGCCAATAGCATCCAGAGCATTCTTGGGATACAGTCGATCGATa                                     >  1:3200216/1‑65 (MQ=255)
                                      cACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTggg                                                     >  1:2950142/1‑49 (MQ=255)
                                      cACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTggg                                                     >  1:680156/1‑49 (MQ=255)
                                      cACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTggg                                                     >  1:1125007/1‑49 (MQ=255)
                                      cACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTggg                                                     >  1:1260421/1‑49 (MQ=255)
                                      cACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTggg                                                     >  1:1439863/1‑49 (MQ=255)
                                      cACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGtcgatcga                                       >  1:2709746/1‑63 (MQ=255)
                                      cACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGa                               <  1:2869304/71‑1 (MQ=255)
                                              ccGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTcggt                       >  1:771534/1‑71 (MQ=255)
                                              ccGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTcggt                       >  1:3354006/1‑71 (MQ=255)
                                              ccGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTcggt                       >  1:272333/1‑71 (MQ=255)
                                                 cgGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTcggtgcg                    <  1:1667436/71‑1 (MQ=255)
                                                    ttCTGAAAGCCAATAGCATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTcggtgcggtg                 <  1:3438840/71‑1 (MQ=255)
                                                      cTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTCGGTGCGGTGAt               >  1:3583548/1‑71 (MQ=255)
                                                      cTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTCGGTGCGGTGAt               >  1:2964947/1‑71 (MQ=255)
                                                      cTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTCGGTGCGGTGAt               >  1:1219479/1‑71 (MQ=255)
                                                            gCCAATAACATCCAGAGCATTCTTGGGATCCAGtcgatc                                         <  1:1843949/39‑1 (MQ=255)
                                                            gCCAATAACATCCAGAGCATTCTTGGGATCCAGtcgatc                                         <  1:1137630/39‑1 (MQ=255)
                                                            gCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTCGGTGCGGTGATCTCCgg         <  1:407818/71‑1 (MQ=255)
                                                            gCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTCGGTGCGGTGATCGCCgg         <  1:1978624/71‑1 (MQ=255)
                                                             ccAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTCGGTGCGGTGATCGCCgg         <  1:2644478/70‑1 (MQ=255)
                                                              cAATAGCATCCAGAGCATTCTTGGGATCCAGTCGATCGATa                                     >  1:124930/1‑41 (MQ=255)
                                                              cAATAGCATCCAGAGCATTCTTGGGATCCAGTCGATCGATa                                     >  1:1117235/1‑41 (MQ=255)
                                                              cAATAGCATCCAGAGCATTCTTGGGATCCAGTCGATCGATa                                     >  1:3398201/1‑41 (MQ=255)
                                                               aaTAGCATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTCGGTGCGGTGATCGCCGGtat      >  1:1459015/1‑71 (MQ=255)
                                                               aaTAGCATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTCGGTGCGGTGATCGCCGGtat      >  1:4073052/1‑71 (MQ=255)
                                                               aaTAGCATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTCGGTGCGGTGATCGCCGGtat      >  1:621791/1‑71 (MQ=255)
                                                               aaTAGCATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTCGGTGCGGTGATCGCCGGtat      >  1:905992/1‑71 (MQ=255)
                                                                aTAGCATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTCGGTGCGGTGATCGCCGGtatt     <  1:1516185/71‑1 (MQ=255)
                                                                 tAACATCCAGAGCATTCTTGGGATCCAGTcgatcgat                                      <  1:242257/37‑1 (MQ=255)
                                                                 tAACATCCAGAGCATTCTTGGGATCCAGTcgatcgat                                      <  1:613755/37‑1 (MQ=255)
                                                                 tAACATCCAGAGCATTCTTGGGATCCAGTcgatcgat                                      <  1:2989040/37‑1 (MQ=255)
                                                                 tAACATCCAGAGCATTCTTGGGATCCAGTcgatcgat                                      <  1:1575193/37‑1 (MQ=255)
                                                                   aCATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTCGGTGCGGTGATCGCCGGTATTATc  <  1:188925/71‑1 (MQ=255)
                                                                   |                                                                      
GTAAACTTCTGGTTGACCAATAAAGGCATTCTGCCAACCACGGATGCCGCGGTTCTGAAAGCCAATAACATCCAGAGCATTCTTGGGATCCAGTCGATCGATACCGGGATCCTCGGTGCGGTGATCGCCGGTATTATC  >  minE/1027379‑1027516

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