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 3,824,368 G→A 100% pseudogene (501/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,824,3680GA96.6% 330.4 / 2.3 117pseudogene (501/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base G (4/0);  new base A (58/55);  total (62/55)
Fisher's exact test for biased strand distribution p-value = 1.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01
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 123 total aligned reads displayed.

GTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTA  >  W3110S.gb/3824300‑3824434
                                                                    |                                                                  
gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa                                                                  >  1:5092178/1‑71 (MQ=255)
   gAAAACGGCAAGCTGAAAACTAATCCAATGAAAGGGATGGTAGCCGCGGTCTCTGTCGGGATTGTGAAc                                                                 >  1:274589/1‑69 (MQ=255)
   gAAAACGGCAAGCTGAAAACTAATCCAATGAAAGGGATGGTAGCCGCGGTCTCTGTCGGGATTGTGAAc                                                                 >  1:5645881/1‑69 (MQ=255)
   gAAAACGGCAAGCTGAAAACTAATCCAATGAAAGGGATGGTAGCCGCGGTCTCTGTCGGGATTGTGAAc                                                                 >  1:5274513/1‑69 (MQ=255)
   gAAAACGGCAAGCTGAAAACTAATCCAATGAAAGGGATGGTAGCCGCGGTCTCTGTCGGGATTGTGAAc                                                                 >  1:1647026/1‑69 (MQ=255)
   gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                                                               <  1:5017540/71‑1 (MQ=255)
   gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                                                               <  1:5008591/71‑1 (MQ=255)
   gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg                                                                <  1:5065569/70‑1 (MQ=255)
    aaaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt                                                              <  1:3385571/71‑2 (MQ=255)
     aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                             <  1:290001/71‑3 (MQ=255)
     aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                             <  1:6904795/71‑3 (MQ=255)
     aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt                                                              <  1:5361074/70‑2 (MQ=255)
      aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                             <  1:6588912/70‑3 (MQ=255)
        cGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAg                                                          >  1:2094442/1‑71 (MQ=255)
        cGGAAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa                                                                  >  1:1198378/1‑63 (MQ=255)
           cAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaa                                                       >  1:7317590/1‑69 (MQ=255)
                tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                             >  1:5880210/1‑58 (MQ=255)
                tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg                                                   >  1:283204/1‑70 (MQ=255)
                 gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                             >  1:456254/1‑57 (MQ=255)
                 gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                             >  1:3933074/1‑57 (MQ=255)
                 gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                             >  1:6074585/1‑57 (MQ=255)
                  aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc                                                  <  1:6098001/69‑1 (MQ=255)
                  aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc                                                  <  1:7254816/69‑1 (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                                               >  1:4029612/1‑71 (MQ=255)
                    aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg                                                                >  1:1849867/1‑53 (MQ=255)
                    aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc                                              >  1:6473557/1‑71 (MQ=255)
                    aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc                                              >  1:4882689/1‑71 (MQ=255)
                    aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc                                              <  1:1446023/71‑1 (MQ=255)
                    aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCCGTCGGTATTGTAAACg                                                                >  1:7571522/1‑53 (MQ=255)
                      ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg                                            >  1:5948571/1‑71 (MQ=255)
                       cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                           <  1:2465982/71‑1 (MQ=255)
                       cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg                                            >  1:341934/1‑70 (MQ=255)
                        aacccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                           >  1:4625934/4‑70 (MQ=255)
                        aacccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                           >  1:6657900/4‑70 (MQ=255)
                        aacccGATGAAAGGGATGGTAGCC‑CAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                         <  1:301614/68‑1 (MQ=255)
                          cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                         >  1:6965927/2‑70 (MQ=255)
                          cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                         >  1:3580140/2‑70 (MQ=255)
                          cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                         >  1:4200866/2‑70 (MQ=255)
                            cGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATAc                                      <  1:6594128/71‑1 (MQ=255)
                             gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa                                                                  >  1:3171418/1‑42 (MQ=38)
                             gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa                                                                  >  1:431653/1‑42 (MQ=38)
                             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)
                                gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                             <  1:7304618/44‑3 (MQ=38)
                                gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                   >  1:2293782/1‑70 (MQ=255)
                                gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                   >  1:2048639/1‑70 (MQ=255)
                                 aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt                                                              <  1:1684897/42‑2 (MQ=38)
                                 aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                           <  1:5964785/61‑1 (MQ=255)
                                  aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAAc                                                                 >  1:2430726/1‑38 (MQ=38)
                                  aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                                     <  1:6044119/66‑1 (MQ=255)
                                       aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                            >  1:1821293/1‑70 (MQ=255)
                                        tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                            >  1:2246464/1‑69 (MQ=255)
                                        tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                            >  1:5108375/1‑69 (MQ=255)
                                         ggTAGCCGCAGTTTCTGTCGGTATTGGAAACGGTGAAGCAATTTGCGAt                                               <  1:7869876/49‑1 (MQ=19)
                                           tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc                       <  1:2234533/71‑1 (MQ=255)
                                             gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                  >  1:732421/1‑58 (MQ=255)
                                             gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGc                     <  1:2720575/71‑1 (MQ=255)
                                               cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg                      >  1:3025637/1‑68 (MQ=255)
                                                gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                <  1:2779687/57‑1 (MQ=255)
                                                gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                <  1:2348016/57‑1 (MQ=255)
                                                gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                <  1:7256803/57‑1 (MQ=255)
                                                gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga                  <  1:7771109/71‑1 (MQ=255)
                                                gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga                  <  1:6906349/71‑1 (MQ=255)
                                                gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                    >  1:2225744/1‑69 (MQ=255)
                                                 cAGTTTCTGTCGGTATTGTAAACTGTGAAGCAATTTGCGATCTTTAATACGTTGAAGACTCAGCCGCagag                 <  1:3740734/71‑1 (MQ=255)
                                                 cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                 <  1:4233017/71‑1 (MQ=255)
                                                 cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                 <  1:5058258/71‑1 (MQ=255)
                                                 cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                 <  1:4794930/71‑1 (MQ=255)
                                                  aGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAgaga                >  1:2589623/1‑71 (MQ=255)
                                                   gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc               >  1:5687211/1‑71 (MQ=255)
                                                   gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc               >  1:1883730/1‑71 (MQ=255)
                                                   gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc               >  1:7425069/1‑71 (MQ=255)
                                                    tttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                   <  1:7923936/50‑1 (MQ=255)
                                                      tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                           >  1:1024869/1‑40 (MQ=16)
                                                      tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                           >  1:7438114/1‑40 (MQ=16)
                                                      tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc               >  1:2439976/1‑68 (MQ=255)
                                                          tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                           <  1:5082583/36‑1 (MQ=12)
                                                          tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                           <  1:1621561/36‑1 (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        <  1:1680565/71‑1 (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)
                                                                    |                                                                  
GTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTA  >  W3110S.gb/3824300‑3824434

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