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 3,824,380 2 bp→AA 100% pseudogene (513‑514/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,824,3800GA100.0% 266.1 / NA 91pseudogene (513/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (50/41);  total (50/41)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
*W3110S.gb3,824,3810GA100.0% 266.7 / NA 91pseudogene (514/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (50/41);  total (50/41)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCG  >  W3110S.gb/3824316‑3824444
                                                                ||                                                               
tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc                                                            >  1:610660/1‑71 (MQ=255)
  aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                           <  1:3496848/70‑1 (MQ=255)
  aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                           <  1:350950/70‑1 (MQ=255)
     aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                           <  1:3361217/67‑1 (MQ=255)
       cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     <  1:1021298/71‑1 (MQ=255)
       cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     <  1:2033232/71‑1 (MQ=255)
       cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGGCGGTATTGTAACCGGTGAAGCAATTTGCGATCTgg                                                     <  1:3730322/71‑1 (MQ=255)
       cAACCCGATG‑AAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     <  1:1766045/70‑1 (MQ=255)
         acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                                   <  1:606789/69‑1 (MQ=255)
          cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                           <  1:3612276/61‑1 (MQ=255)
           ccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                                          >  1:211847/1‑62 (MQ=255)
           ccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                         >  1:2570181/1‑63 (MQ=255)
           ccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                         >  1:1648232/1‑63 (MQ=255)
           ccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                         >  1:2002473/1‑63 (MQ=255)
               tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATa                                                 <  1:2110420/67‑1 (MQ=255)
               tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATa                                                 <  1:4010269/67‑1 (MQ=255)
               tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGCAATa                                                 <  1:1312683/67‑1 (MQ=255)
                gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                             >  1:3640234/1‑70 (MQ=255)
                  aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                          <  1:695342/71‑1 (MQ=255)
                    gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                                   >  1:2627856/1‑60 (MQ=255)
                    gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGa                                        >  1:3939322/1‑71 (MQ=255)
                       aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     <  1:2792880/55‑1 (MQ=255)
                          gTAGCCTCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                          <  1:550/63‑1 (MQ=255)
                          gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                           <  1:2418701/46‑1 (MQ=25)
                          gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                          >  1:3337982/1‑63 (MQ=255)
                          gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                          >  1:4070183/1‑63 (MQ=255)
                          gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                          >  1:3494366/1‑63 (MQ=255)
                          gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                          >  1:681364/1‑63 (MQ=255)
                          gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                  >  1:2409979/1‑71 (MQ=255)
                           tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                                          >  1:1793118/1‑46 (MQ=25)
                           tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                                          >  1:841309/1‑46 (MQ=25)
                           tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                                          >  1:1723619/1‑46 (MQ=25)
                           tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc                                 >  1:3234946/1‑71 (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)
                               cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg                                >  1:975391/1‑68 (MQ=255)
                                     ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                        >  1:3221884/1‑70 (MQ=255)
                                      tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGa                                                    >  1:3889590/1‑41 (MQ=19)
                                      tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                      >  1:3724334/1‑71 (MQ=255)
                                      tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                      >  1:1003676/1‑71 (MQ=255)
                                      tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                      >  1:2713519/1‑71 (MQ=255)
                                      tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                      >  1:107740/1‑71 (MQ=255)
                                      tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                      >  1:1253759/1‑71 (MQ=255)
                                      tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                      >  1:806512/1‑71 (MQ=255)
                                      tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                      >  1:2740603/1‑71 (MQ=255)
                                            ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                >  1:1427256/4‑71 (MQ=255)
                                              taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                              <  1:625363/54‑1 (MQ=255)
                                              taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                              <  1:3338627/54‑1 (MQ=255)
                                                ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                             <  1:1858261/38‑1 (MQ=21)
                                                ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                             <  1:2071848/38‑1 (MQ=21)
                                                ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                             <  1:2361327/38‑1 (MQ=21)
                                                ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                             <  1:2484554/38‑1 (MQ=21)
                                                ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg              >  1:1263306/1‑69 (MQ=255)
                                                 tgtaAACGGTGAAGCAATTTGCGATCTGGAATTCGtt                                             <  1:3684138/37‑1 (MQ=12)
                                                 tgtaAACGGTCAAGCAATTTGCGATCTGGAATACGtt                                             <  1:602387/37‑1 (MQ=12)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGAc                     >  1:851383/4‑60 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:908874/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:9525/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:49176/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:489704/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:1016059/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:3616225/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:3232911/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:127790/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:3151080/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:1316820/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:1322062/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:1325536/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:1350753/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:1530920/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:2187513/4‑71 (MQ=255)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          >  1:2265045/4‑71 (MQ=255)
                                                   taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg         <  1:3213145/69‑1 (MQ=255)
                                                   taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          <  1:3391885/68‑1 (MQ=255)
                                                   taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          <  1:1949343/68‑1 (MQ=255)
                                                   taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          <  1:600399/68‑1 (MQ=255)
                                                   taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          <  1:2532040/68‑1 (MQ=255)
                                                     aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat       <  1:600091/71‑1 (MQ=255)
                                                     aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat       >  1:2344563/1‑71 (MQ=255)
                                                     aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat       <  1:2500666/71‑1 (MQ=255)
                                                     aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat       >  1:2907660/1‑71 (MQ=255)
                                                      aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatg      <  1:160252/71‑1 (MQ=255)
                                                       cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatga     >  1:2882294/1‑71 (MQ=255)
                                                         gtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          <  1:1444111/62‑1 (MQ=255)
                                                         gtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          <  1:441298/62‑1 (MQ=255)
                                                         gtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          <  1:3173881/62‑1 (MQ=255)
                                                         gtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt          <  1:1148953/62‑1 (MQ=255)
                                                          tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg  <  1:685252/70‑1 (MQ=255)
                                                          tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg  <  1:791287/70‑1 (MQ=255)
                                                                ||                                                               
TGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCG  >  W3110S.gb/3824316‑3824444

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