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 F1 I0 R2 201 99.6 7939938 96.9% 7693799 60.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,824,374 C→T 100% pseudogene (507/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,824,3740CT100.0% 324.7 / NA 111pseudogene (507/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (52/59);  total (52/59)
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 111 total aligned reads displayed.

AACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGA  >  W3110S.gb/3824306‑3824441
                                                                    |                                                                   
  cGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAg                                                                 >  1:2094442/1‑71 (MQ=255)
     cAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaa                                                              >  1:7317590/1‑69 (MQ=255)
          tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg                                                          >  1:283204/1‑70 (MQ=255)
            aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc                                                         <  1:7254816/69‑1 (MQ=255)
            aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc                                                         <  1:6098001/69‑1 (MQ=255)
            aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                        >  1:5650125/1‑70 (MQ=255)
            aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                        >  1:604213/1‑70 (MQ=255)
            aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                                       >  1:1628997/1‑71 (MQ=255)
            aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                                       >  1:2190134/1‑71 (MQ=255)
             aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCTAt                                                      <  1:497281/71‑1 (MQ=255)
             aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                      >  1:7566278/1‑71 (MQ=255)
             aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                      <  1:1508906/71‑1 (MQ=255)
             aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                      >  1:4029612/1‑71 (MQ=255)
             aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                      >  1:6214607/1‑71 (MQ=255)
              aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc                                                     <  1:1446023/71‑1 (MQ=255)
              aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc                                                     >  1:4882689/1‑71 (MQ=255)
              aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc                                                     >  1:6473557/1‑71 (MQ=255)
                ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg                                                   >  1:5948571/1‑71 (MQ=255)
                 cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  <  1:827168/71‑1 (MQ=255)
                 cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  <  1:4420449/71‑1 (MQ=255)
                 cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  <  1:2465982/71‑1 (MQ=255)
                 cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  <  1:253669/71‑1 (MQ=255)
                 cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg                                                   >  1:341934/1‑70 (MQ=255)
                  aacccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  >  1:4625934/4‑70 (MQ=255)
                  aacccGATGAAAGGGATGGTAGCC‑CAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                                <  1:301614/68‑1 (MQ=255)
                    cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                                >  1:6965927/2‑70 (MQ=255)
                    cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                                >  1:4200866/2‑70 (MQ=255)
                    cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                                >  1:3580140/2‑70 (MQ=255)
                      cGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATAc                                             <  1:6594128/71‑1 (MQ=255)
                       gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                                            <  1:1402161/71‑1 (MQ=255)
                        aTGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa                                                                  >  1:1272894/1‑48 (MQ=255)
                        aTGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa                                                                  >  1:2651908/1‑48 (MQ=255)
                         tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg                                                   >  1:2157606/1‑62 (MQ=255)
                         tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                          >  1:3134025/1‑71 (MQ=255)
                          gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                          >  1:2048639/1‑70 (MQ=255)
                          gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                          >  1:2293782/1‑70 (MQ=255)
                           aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  <  1:5964785/61‑1 (MQ=255)
                           aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                         <  1:2334746/70‑1 (MQ=255)
                            aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                                            <  1:6044119/66‑1 (MQ=255)
                                 aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActc                                  <  1:4917891/71‑1 (MQ=255)
                                 aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                                   >  1:1821293/1‑70 (MQ=255)
                                  tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                                       >  1:4007349/1‑49 (MQ=25)
                                  tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                                   >  1:5108375/1‑69 (MQ=255)
                                  tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                                   >  1:2246464/1‑69 (MQ=255)
                                   ggTAGCCGCAGTTTCTGTCGGTATTGGAAACGGTGAAGCAATTTGCGAt                                                      <  1:7869876/49‑1 (MQ=19)
                                    gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActcag                                <  1:2034988/70‑3 (MQ=255)
                                       gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                         >  1:732421/1‑58 (MQ=255)
                                       gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGc                            <  1:2720575/71‑1 (MQ=255)
                                          gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                       <  1:2779687/57‑1 (MQ=255)
                                          gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                       <  1:2348016/57‑1 (MQ=255)
                                          gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                       <  1:7256803/57‑1 (MQ=255)
                                          gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga                         <  1:6906349/71‑1 (MQ=255)
                                          gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga                         <  1:7771109/71‑1 (MQ=255)
                                          gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                           >  1:2225744/1‑69 (MQ=255)
                                           cAGTTTCTGTCGGTATTGTAAACTGTGAAGCAATTTGCGATCTTTAATACGTTGAAGACTCAGCCGCagag                        <  1:3740734/71‑1 (MQ=255)
                                           cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                        <  1:4233017/71‑1 (MQ=255)
                                           cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                        <  1:4794930/71‑1 (MQ=255)
                                           cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                        <  1:5058258/71‑1 (MQ=255)
                                             gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGc                            >  1:5667497/1‑65 (MQ=255)
                                             gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                      >  1:1883730/1‑71 (MQ=255)
                                             gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                      >  1:7425069/1‑71 (MQ=255)
                                             gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                      >  1:5687211/1‑71 (MQ=255)
                                              tttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                          <  1:7923936/50‑1 (MQ=255)
                                                tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  >  1:7438114/1‑40 (MQ=16)
                                                tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  >  1:1024869/1‑40 (MQ=16)
                                                tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                      >  1:2439976/1‑68 (MQ=255)
                                                    tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  <  1:1621561/36‑1 (MQ=12)
                                                    tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  <  1:5082583/36‑1 (MQ=12)
                                                    tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  <  1:2514973/36‑1 (MQ=12)
                                                    tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  <  1:2615448/36‑1 (MQ=12)
                                                    tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACAt                >  1:1568529/1‑70 (MQ=255)
                                                    tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACAt                >  1:6175232/1‑70 (MQ=255)
                                                    tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg               <  1:1671366/71‑1 (MQ=255)
                                                    tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACC‑ACATg               <  1:3435336/70‑1 (MQ=255)
                                                     cGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                      >  1:4989220/1‑63 (MQ=255)
                                                      ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa              <  1:2624338/67‑1 (MQ=255)
                                                        taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg           >  1:7038369/2‑71 (MQ=255)
                                                          ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                                   <  1:3002219/45‑1 (MQ=25)
                                                          ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa         <  1:3721873/71‑1 (MQ=255)
                                                           tgtaAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                                   <  1:4321038/44‑1 (MQ=25)
                                                           tgtaAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                                   <  1:7823336/44‑1 (MQ=25)
                                                            gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAg        <  1:7020579/67‑1 (MQ=255)
                                                             taaaCGGTGAAGCAATTTGCGATTTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       <  1:4663940/68‑1 (MQ=255)
                                                             taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCTCAGAGACCGACATGAACGTAGt       <  1:6996966/68‑1 (MQ=255)
                                                             taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                     <  1:30812/54‑1 (MQ=255)
                                                             taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                     <  1:1410926/54‑1 (MQ=255)
                                                             taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg      <  1:1857386/69‑1 (MQ=255)
                                                             taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       <  1:290579/68‑1 (MQ=255)
                                                             taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       <  1:5813970/68‑1 (MQ=255)
                                                              aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga     >  1:3040612/2‑71 (MQ=255)
                                                              aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg      <  1:2235361/69‑1 (MQ=255)
                                                               aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCag                          >  1:5588589/1‑49 (MQ=37)
                                                               aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAg        <  1:7497985/67‑1 (MQ=255)
                                                                aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatg   <  1:5144727/71‑1 (MQ=255)
                                                                aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat    >  1:3047692/1‑70 (MQ=255)
                                                                 cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg                    <  1:6044309/53‑1 (MQ=255)
                                                                 cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg                    <  1:5649620/53‑1 (MQ=255)
                                                                 cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                   >  1:4620357/1‑54 (MQ=255)
                                                                 cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatga  <  1:6593615/71‑1 (MQ=255)
                                                                 cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatga  >  1:4519624/1‑71 (MQ=255)
                                                                    |                                                                   
AACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGA  >  W3110S.gb/3824306‑3824441

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A