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
A1 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,824,410 T→A 100% pseudogene (543/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,824,4100TA100.0% 315.8 / NA 107pseudogene (543/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (59/48);  total (59/48)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

Only 100 of 108 total aligned reads displayed.

GTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGACGG  >  W3110S.gb/3824342‑3824477
                                                                    |                                                                   
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                                                   >  1:2409979/1‑71 (MQ=255)
 tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc                                                                  >  1:3556558/1‑71 (MQ=255)
   gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg                                                                 <  1:363868/70‑1 (MQ=255)
    ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                                                               <  1:3462913/71‑1 (MQ=255)
    ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                                                               <  1:3884274/71‑1 (MQ=255)
           ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                                         >  1:3221884/1‑70 (MQ=255)
            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                                                       >  1:1003676/1‑71 (MQ=255)
            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                                                       >  1:107740/1‑71 (MQ=255)
            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                                                       >  1:1253759/1‑71 (MQ=255)
            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                                                       >  1:806512/1‑71 (MQ=255)
            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                                                       >  1:2713519/1‑71 (MQ=255)
            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                                                       >  1:2740603/1‑71 (MQ=255)
                  ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                                                 >  1:1427256/4‑71 (MQ=255)
                    taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                                                               <  1:625363/54‑1 (MQ=255)
                    taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                                                               <  1:3338627/54‑1 (MQ=255)
                      ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                                               >  1:1263306/1‑69 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGAc                                                      >  1:851383/4‑60 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:2187513/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:3616225/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:908874/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:2265045/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:49176/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:489704/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:3151080/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:3232911/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:1016059/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:1530920/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:127790/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:1316820/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:9525/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:1322062/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:1350753/4‑71 (MQ=255)
                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:1325536/4‑71 (MQ=255)
                         taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg                                          <  1:3213145/69‑1 (MQ=255)
                         taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           <  1:2532040/68‑1 (MQ=255)
                         taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           <  1:1949343/68‑1 (MQ=255)
                         taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           <  1:3391885/68‑1 (MQ=255)
                           aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat                                        >  1:2344563/1‑71 (MQ=255)
                           aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat                                        <  1:2500666/71‑1 (MQ=255)
                           aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat                                        <  1:600091/71‑1 (MQ=255)
                           aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat                                        >  1:2907660/1‑71 (MQ=255)
                            aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatg                                       <  1:160252/71‑1 (MQ=255)
                             cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatga                                      >  1:2882294/1‑71 (MQ=255)
                               gtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           <  1:1148953/62‑1 (MQ=255)
                               gtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           <  1:441298/62‑1 (MQ=255)
                               gtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           <  1:1444111/62‑1 (MQ=255)
                               gtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           <  1:3173881/62‑1 (MQ=255)
                                tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg                                   <  1:685252/70‑1 (MQ=255)
                                tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg                                   <  1:791287/70‑1 (MQ=255)
                                     caatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGAc                              <  1:1418340/68‑1 (MQ=255)
                                     caatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGAc                              <  1:1297716/68‑1 (MQ=255)
                                        tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa                                                  <  1:3977292/48‑1 (MQ=255)
                                        tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa                                                  <  1:3114597/48‑1 (MQ=255)
                                        tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                                               <  1:3893572/51‑1 (MQ=255)
                                        tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                                               <  1:3730197/51‑1 (MQ=255)
                                        tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                                               <  1:937282/51‑1 (MQ=255)
                                        tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa                                 <  1:1827484/65‑1 (MQ=255)
                                          tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGCCCGACATGAACGTAGTGATGACCGAAGACGGgcg                         >  1:1594272/1‑71 (MQ=255)
                                          tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGa                               >  1:2644748/1‑65 (MQ=255)
                                          tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGa                               >  1:1278933/1‑65 (MQ=255)
                                          tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGa                               >  1:1235883/1‑65 (MQ=255)
                                          tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGa                               >  1:2452814/1‑65 (MQ=255)
                                           gCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACgggag                         <  1:1395305/70‑3 (MQ=255)
                                              aTCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           >  1:1292398/1‑49 (MQ=255)
                                                   gAATACGTTGAAGACTGAGCCGCAGAGACCGACATGAACGTAGt                                           <  1:584753/44‑1 (MQ=255)
                                                   gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGATCGTAGt                                           <  1:3116243/44‑1 (MQ=255)
                                                   gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           <  1:24965/44‑1 (MQ=255)
                                                   gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg                 <  1:4009969/70‑1 (MQ=255)
                                                   gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg                 >  1:1031570/1‑70 (MQ=255)
                                                   gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg                 >  1:3547823/1‑70 (MQ=255)
                                                    aaTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcat                      <  1:2331701/64‑1 (MQ=255)
                                                      tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt                                              <  1:1009102/38‑1 (MQ=255)
                                                      tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat                                        <  1:2408274/44‑1 (MQ=255)
                                                      tACCTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat                                        <  1:3873581/44‑1 (MQ=255)
                                                       aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                           <  1:772295/40‑1 (MQ=255)
                                                        cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga                                         >  1:9543/1‑41 (MQ=255)
                                                        cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga                                         >  1:3662077/1‑41 (MQ=255)
                                                        cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga                                         >  1:1893676/1‑41 (MQ=255)
                                                        cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga                                         >  1:2192731/1‑41 (MQ=255)
                                                        cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga                                         >  1:3155780/1‑41 (MQ=255)
                                                        cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga                                         >  1:719078/1‑41 (MQ=255)
                                                        cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg                                   <  1:1077260/47‑1 (MQ=255)
                                                        cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg                                   <  1:3428782/47‑1 (MQ=255)
                                                        cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg                                   <  1:3044257/47‑1 (MQ=255)
                                                        cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGAc                              >  1:2485645/1‑52 (MQ=255)
                                                        cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTg            <  1:274953/70‑1 (MQ=255)
                                                        cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTg            >  1:343457/1‑70 (MQ=255)
                                                        cGTTGAAGACTCAGCCGCAGAGACAGACATGAACg                                               >  1:2605933/1‑35 (MQ=38)
                                                         gTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa                                 >  1:2465078/1‑48 (MQ=255)
                                                         gTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa                                 >  1:2450882/1‑48 (MQ=255)
                                                         gTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa                                 >  1:3744104/1‑48 (MQ=255)
                                                         gTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa                                 >  1:1768957/1‑48 (MQ=255)
                                                          ttGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg                                   <  1:1831116/45‑1 (MQ=255)
                                                          ttGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatca                    <  1:2962022/60‑1 (MQ=255)
                                                             aaGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg                 <  1:3176306/60‑1 (MQ=255)
                                                             aaGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg                 <  1:3510619/60‑1 (MQ=255)
                                                             aaGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGG‑‑GCATCATTGAAGTGCAGGGGAc    <  1:3601628/71‑1 (MQ=255)
                                                              aGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa                                 <  1:783079/43‑1 (MQ=255)
                                                              aGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg                 <  1:2252430/59‑1 (MQ=255)
                                                                 ctcaGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGACgg  >  1:4046918/1‑71 (MQ=255)
                                                                    |                                                                   
GTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGACGG  >  W3110S.gb/3824342‑3824477

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