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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,919,210 T→C 23.7% A162A (GCA→GCG)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,2100TC23.7% 206.3 / 66.2 114A162A (GCA→GCG) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base T (39/48);  new base C (17/10);  total (56/58)
Fisher's exact test for biased strand distribution p-value = 1.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

Only 100 of 117 total aligned reads displayed.

GACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATC  >  minE/2919140‑2919275
                                                                      |                                                                 
gACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCt                                                                   >  1:3557828/1‑71 (MQ=255)
gACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCt                                                                   >  1:282821/1‑71 (MQ=255)
 ccGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTg                                                                  >  1:652588/2‑71 (MQ=255)
  cGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGc                                                                 <  1:1517398/71‑1 (MQ=255)
   gCAGATCCAGCCCGGTCAGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGcg                                                                >  1:2437121/1‑70 (MQ=255)
    cAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCAt                                                               <  1:2048631/71‑1 (MQ=255)
     agaTCCAGCCCGGTCAGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTa                                                              <  1:1072696/69‑1 (MQ=255)
     aaaTCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCa                                                                >  1:2616502/1‑69 (MQ=255)
     aaaTCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATa                                                              <  1:3293749/71‑1 (MQ=255)
      aaTCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAg                                                             <  1:3413603/71‑1 (MQ=255)
       aTCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCGATGTTGTTACGCGCGTCACCTGCATAg                                                             <  1:1724833/70‑1 (MQ=255)
       aTCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGa                                                            >  1:992121/1‑71 (MQ=255)
       aTCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGa                                                            >  1:2904147/1‑71 (MQ=255)
          cAGCCCGGTCAGCGCGGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGAc                                                           >  1:2948535/1‑69 (MQ=255)
            gACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGc                                                       >  1:1582406/1‑71 (MQ=255)
             acaggTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCg                                                      >  1:18140/4‑71 (MQ=255)
             aCCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCa                                                         <  1:383810/68‑1 (MQ=255)
              ccGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGt                                                     <  1:205712/71‑1 (MQ=255)
                 gtcaGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCAt                                                  >  1:371926/4‑71 (MQ=255)
                   aaGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGAc                                                           >  1:2726544/1‑60 (MQ=255)
                   aaGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTc                                                    >  1:3090568/1‑67 (MQ=255)
                   aaGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCAttt                                                >  1:721565/1‑71 (MQ=255)
                    aGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTc                                               >  1:3935842/1‑71 (MQ=255)
                    aGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTc                                               <  1:910884/71‑1 (MQ=255)
                    aGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGAATAGACCAGCGTCATTTc                                               >  1:2800822/1‑71 (MQ=255)
                      cgccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGGCACCTGCATAGACCAGCGTCATTTCGt                                             <  1:1808402/71‑1 (MQ=255)
                        ccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTg                                           <  1:1578336/71‑1 (MQ=255)
                         cgcAGCTTCGAGCATCGAATTGCCCATGTTGTTAGGCGCGTCACCt                                                                   <  1:1501341/46‑1 (MQ=255)
                          gcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGttaac                                         >  1:3249707/1‑68 (MQ=255)
                            aGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACg                                       >  1:910126/1‑71 (MQ=255)
                             gCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGc                                      >  1:2102341/1‑71 (MQ=255)
                              cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGc                                                                 <  1:3952579/43‑1 (MQ=255)
                              cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                     <  1:1992691/71‑1 (MQ=255)
                              cTTCGAGCAGCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGt                                             <  1:361106/63‑1 (MQ=255)
                              cTTCGAGCAGCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGt                                             <  1:365812/63‑1 (MQ=255)
                               ttCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCtt                                    >  1:1581253/1‑71 (MQ=255)
                               ttCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCtt                                    >  1:1117797/1‑71 (MQ=255)
                                tCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCa                                                                >  1:2467971/1‑42 (MQ=255)
                                tCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTg                                           >  1:1166324/1‑63 (MQ=255)
                                tCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTg                                           >  1:2810286/1‑63 (MQ=255)
                                 ccaGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTg                                  >  1:2974639/3‑71 (MQ=255)
                                 cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                   <  1:839445/70‑1 (MQ=255)
                                 cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                   <  1:299123/70‑1 (MQ=255)
                                 cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                     >  1:3850122/1‑68 (MQ=255)
                                 cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                     >  1:3835298/1‑68 (MQ=255)
                                  gAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTg                                  <  1:3146009/70‑1 (MQ=255)
                                     cATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCg                                                      <  1:2930009/47‑1 (MQ=255)
                                     cATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGcccg                              >  1:3841291/1‑69 (MQ=255)
                                     cATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCg                               <  1:694927/70‑1 (MQ=255)
                                      aTCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGcc                                >  1:1172768/1‑68 (MQ=255)
                                       tCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTc                                                    >  1:1320609/1‑47 (MQ=255)
                                       tCGAGTTGCCCATGTTGTTGCGCGCATAGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCctt                                   >  1:1901390/1‑64 (MQ=255)
                                         gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaa                          <  1:2893689/71‑1 (MQ=255)
                                         gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaa                          <  1:762208/71‑1 (MQ=255)
                                         gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa                           <  1:58346/70‑1 (MQ=255)
                                         gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa                           <  1:2583324/70‑1 (MQ=255)
                                          aaTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGcc                                <  1:1063702/64‑1 (MQ=255)
                                          aaTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaaa                         <  1:3235175/71‑1 (MQ=255)
                                          aaTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaaa                         >  1:3741343/1‑71 (MQ=255)
                                           gttGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTaaa                                         >  1:82953/2‑54 (MQ=255)
                                           aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCAtt                                                 <  1:890348/46‑1 (MQ=255)
                                           aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAAc                                        <  1:3546383/55‑1 (MQ=255)
                                           aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAAc                                        <  1:668902/55‑1 (MQ=255)
                                           aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAAc                                        <  1:2687687/55‑1 (MQ=255)
                                             tGCCCATGTTGTTGCACGCATCGCCCGCGTAGACCAGCGTCATATCGTTAAACGc                                      >  1:1316265/1‑55 (MQ=255)
                                              gCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                   >  1:2686168/1‑57 (MQ=255)
                                              gCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCt                     >  1:554028/1‑71 (MQ=255)
                                               cccATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGc                            <  1:3755735/63‑1 (MQ=255)
                                                ccATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTcc                   <  1:3782032/71‑1 (MQ=255)
                                                 cATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCt                  >  1:3347436/1‑71 (MQ=255)
                                                  aTGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTg                 <  1:1265581/71‑1 (MQ=255)
                                                  aTGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGc                      <  1:2935722/66‑1 (MQ=255)
                                                   tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTc                                               <  1:243703/40‑1 (MQ=255)
                                                   tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTc                    >  1:2627365/1‑67 (MQ=255)
                                                   tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTg                 >  1:2860423/1‑70 (MQ=255)
                                                   tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTg                 >  1:793078/1‑70 (MQ=255)
                                                     ttgttgCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCa               <  1:1330796/70‑1 (MQ=255)
                                                     ttgttgCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCa               <  1:2089736/70‑1 (MQ=255)
                                                     ttgttgCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCa               <  1:789498/70‑1 (MQ=255)
                                                     ttgttgCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCAt              >  1:1159080/1‑71 (MQ=255)
                                                     ttgttACGCGCGTCACCTGCATAGACAAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGAAt              >  1:1735195/1‑71 (MQ=255)
                                                      tgttGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATg             >  1:2304940/1‑71 (MQ=255)
                                                      tgttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCAt              <  1:465540/70‑1 (MQ=255)
                                                      tgttACGCGCGTCACCTGCATAGACAAGCGTCAttt                                                >  1:1518977/1‑36 (MQ=255)
                                                       gttGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATgg            >  1:2865924/1‑71 (MQ=255)
                                                       gttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATg             <  1:2745274/70‑1 (MQ=255)
                                                        ttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATgg            <  1:358280/70‑1 (MQ=255)
                                                        ttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGt           <  1:1745529/71‑1 (MQ=255)
                                                          gcgcgcaTCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCa                           >  1:428561/2‑53 (MQ=255)
                                                          gcgcgcaTCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCa                           >  1:3906515/2‑53 (MQ=255)
                                                          aCGCGCGTCACCTGCATAGACCAGCGTCATTTCGtt                                            >  1:861328/1‑36 (MQ=255)
                                                          aCGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGt           >  1:291980/1‑69 (MQ=255)
                                                          aCGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTg          <  1:3118263/70‑1 (MQ=255)
                                                           cgcgcaTCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGtca         <  1:414890/70‑3 (MQ=255)
                                                            gcgcgTCACCTGCATAGACAAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTgag        >  1:3389424/1‑70 (MQ=255)
                                                              gcgTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa                           <  1:124757/49‑1 (MQ=255)
                                                                 tCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATc  <  1:984147/71‑1 (MQ=255)
                                                                   aCCTGCATAGACCAGCGTCATTTCGTTGAACGCtt                                    >  1:331443/1‑35 (MQ=255)
                                                                   aCCTGCATAGACCAGCGTCATTTCGTTGAACGCtt                                    >  1:3142143/1‑35 (MQ=255)
                                                                     cTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGagaaga    <  1:1332913/65‑1 (MQ=255)
                                                                      |                                                                 
GACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATC  >  minE/2919140‑2919275

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