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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,939,735 A→G 31.6% A119A (GCT→GCC)  ygfX ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,939,7350AG31.6% 89.9 / 52.6 104A119A (GCT→GCC) ygfXhypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (55/16);  new base G (11/22);  total (66/38)
Fisher's exact test for biased strand distribution p-value = 2.32e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.81e-01

Only 100 of 104 total aligned reads displayed.

TGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACGC  >  minE/1939668‑1939801
                                                                   |                                                                  
tGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAg                                                                   >  1:1603302/1‑69 (MQ=255)
tGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAg                                                                   >  1:1026380/1‑69 (MQ=255)
tGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAg                                                                   >  1:3414267/1‑69 (MQ=255)
tGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAg                                                                   >  1:759872/1‑69 (MQ=255)
tGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAg                                                                   >  1:107032/1‑69 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAATAATATCCGCCGTAAATCCCGCCATTCGGCt                                                                 >  1:1058813/1‑69 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGc                                                                  >  1:1154348/1‑68 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGc                                                                  >  1:1968058/1‑68 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                                                 >  1:21271/1‑69 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                                                 >  1:3123728/1‑69 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                                                 >  1:3389589/1‑69 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                                                 >  1:1741053/1‑69 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                                                 >  1:1491724/1‑69 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                                                 >  1:3414732/1‑69 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                                                 >  1:2186296/1‑69 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGc                                                                  <  1:2166002/68‑1 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGc                                                                  <  1:2065872/68‑1 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGc                                                                  <  1:2900586/68‑1 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGc                                                                  <  1:1936284/68‑1 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGc                                                                  <  1:3268595/68‑1 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGc                                                                  <  1:1551740/68‑1 (MQ=255)
  cTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGc                                                                  <  1:1372495/68‑1 (MQ=255)
  cTTTCCCGTCATCTCTATCTTTGCGTCTCTTGTTGTAACAATATCCGCCGTAAATCCCGCCATTCGGCt                                                                 >  1:1743491/1‑69 (MQ=255)
        cGTCATCTTTATCTTTGCGTCTCTTGTTTCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTc                                                            <  1:1995561/68‑1 (MQ=255)
        cGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTc                                                            <  1:2652274/68‑1 (MQ=255)
         gTCATCTTTATCTTTGCGTCTCTTGTTTCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCa                                                          >  1:3140356/1‑69 (MQ=255)
         gTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTcc                                                           >  1:611001/1‑68 (MQ=255)
         gTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCa                                                          >  1:2044772/1‑69 (MQ=255)
         gTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCa                                                          >  1:2792661/1‑69 (MQ=255)
         gTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCa                                                          >  1:2442512/1‑69 (MQ=255)
            atctttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGc                                                       >  1:1872775/1‑69 (MQ=255)
            atctttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGc                                                       >  1:383169/1‑69 (MQ=255)
            atctttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGc                                                       >  1:1062398/1‑69 (MQ=255)
            atctttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGc                                                       >  1:496198/1‑69 (MQ=255)
            atctttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGc                                                       >  1:1814961/1‑69 (MQ=255)
            atctttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGc                                                       >  1:3358323/1‑69 (MQ=255)
            atctttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGc                                                       >  1:2032292/1‑69 (MQ=255)
               tttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGt                                                    >  1:1117295/1‑69 (MQ=255)
               tttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGt                                                    >  1:2107925/1‑69 (MQ=255)
               tttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGt                                                    >  1:2272006/1‑69 (MQ=255)
               tttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGt                                                    >  1:2394858/1‑69 (MQ=255)
               tttatctttGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGt                                                    >  1:2825558/1‑69 (MQ=255)
               tttatctttGCGTCTCTTGTT‑CAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTc                                                   >  1:1777330/1‑69 (MQ=255)
                           tctcTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagc                                         >  1:2734350/1‑68 (MQ=255)
                           tctcTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagc                                         >  1:934226/1‑68 (MQ=255)
                             tctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagcca                                       >  1:2686575/1‑68 (MQ=255)
                             tctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagcca                                       >  1:2736027/1‑68 (MQ=255)
                             tctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagcca                                       >  1:532068/1‑68 (MQ=255)
                             tctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagcca                                       >  1:196495/1‑68 (MQ=255)
                             tctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagcca                                       >  1:249123/1‑68 (MQ=255)
                             tctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagcca                                       >  1:3426486/1‑68 (MQ=255)
                              ctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCt                                                                 >  1:1227688/1‑41 (MQ=255)
                              ctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTc                                                               >  1:970265/1‑43 (MQ=255)
                              ctTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTc                                                               >  1:1140517/1‑43 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:1979503/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:1540374/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:1793089/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:3284130/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:1352534/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:3217365/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:447577/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:1891364/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:1202710/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:299199/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:2946359/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:2811412/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:524386/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:2025229/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:2360822/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:1063873/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:2155303/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:1084499/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGTCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:533423/66‑1 (MQ=255)
                                    gtaacaaTATCCGCCGTAAATCCCGCCATTCGGCTTCGGCCATGCTGTCAGCTGCCAGCCATAAATGt                                <  1:234714/66‑1 (MQ=255)
                                           aaTCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGttt                        <  1:175261/69‑1 (MQ=255)
                                           aaTCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGttt                        <  1:2033137/69‑1 (MQ=255)
                                            aTCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGttt                        <  1:2926277/68‑1 (MQ=255)
                                               cgccgTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTAcc                     >  1:3097500/1‑68 (MQ=255)
                                               cgccgTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTAcc                     >  1:2245343/1‑68 (MQ=255)
                                               cgccgTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTAcc                     >  1:1158803/1‑68 (MQ=255)
                                               cgccgTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTAc                      >  1:2438848/1‑67 (MQ=255)
                                                            gCCATTCAGCTTCGTCCATGCTGTCGGCTGCCATCCATAAATGTTGCCGTTTACCGCCATCAGAACGTa       <  1:3366316/69‑1 (MQ=255)
                                                            gCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTa       <  1:1959968/69‑1 (MQ=255)
                                                            gCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTa       <  1:231791/69‑1 (MQ=255)
                                                            gCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTa       <  1:1622806/69‑1 (MQ=255)
                                                                  cAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCTGAACGTAAACgc  >  1:3219304/1‑68 (MQ=255)
                                                                  cAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACgc  >  1:776755/1‑68 (MQ=255)
                                                                  cAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACgc  >  1:1062322/1‑68 (MQ=255)
                                                                  cAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACgc  >  1:143458/1‑68 (MQ=255)
                                                                  cAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACgc  >  1:1806941/1‑68 (MQ=255)
                                                                  cAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACgc  >  1:3207574/1‑68 (MQ=255)
                                                                  cAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACgc  >  1:1915368/1‑68 (MQ=255)
                                                                  cAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACgc  >  1:1986869/1‑68 (MQ=255)
                                                                  cAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACgc  >  1:206027/1‑68 (MQ=255)
                                                                  cAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACgc  >  1:2134457/1‑68 (MQ=255)
                                                                  cAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACgc  >  1:2594921/1‑68 (MQ=255)
                                                                  cAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACgc  >  1:2557579/1‑68 (MQ=255)
                                                                  cAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACgc  >  1:2304986/1‑68 (MQ=255)
                                                                  cAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACg   >  1:2382139/1‑67 (MQ=255)
                                                                  cAGCTTCGTCCATCCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACgc  >  1:266415/1‑68 (MQ=255)
                                                                   |                                                                  
TGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACGC  >  minE/1939668‑1939801

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A