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 999,500 G→T 31.5% intergenic (+125/‑151) asr → / → ydgD acid shock‑inducible periplasmic protein/predicted peptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE999,5000GT31.5% 144.0 / 70.3 114intergenic (+125/‑151)asr/ydgDacid shock‑inducible periplasmic protein/predicted peptidase
Reads supporting (aligned to +/- strand):  ref base G (38/40);  new base T (17/19);  total (55/59)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.28e-01

Only 100 of 115 total aligned reads displayed.

GTAACGTTTAGCACCGCCTTTAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTGAT  >  minE/999434‑999566
                                                                  |                                                                  
gTAACGTTTAGCACCGCCTTTAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTGat                                                                  >  1:847923/1‑69 (MQ=255)
gTAACGTTTAGCACCGCCTTTAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTGat                                                                  >  1:267586/1‑69 (MQ=255)
gTAACGTTTAGCACCGCCTTTAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTGat                                                                  >  1:1969535/1‑69 (MQ=255)
gTAACGTTTAGCACCGCCTTTAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTGat                                                                  >  1:1345167/1‑69 (MQ=255)
gTAACGTTTAGCACCGCCTTTAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTGat                                                                  >  1:1811314/1‑69 (MQ=255)
gTAACGTTTAGCACCGCCTTTAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTGat                                                                  >  1:176303/1‑69 (MQ=255)
      tttAGCACCGCCTTTAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTGATCATCCt                                                            <  1:1299051/69‑1 (MQ=255)
      tttAGCACCGCCTTTAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTGATCATCCt                                                            <  1:335608/69‑1 (MQ=255)
      tttAGCACCGCCTTTAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTGATCATCCt                                                            <  1:1703941/69‑1 (MQ=255)
                  tttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:2943180/69‑1 (MQ=255)
                  tttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:2320070/69‑1 (MQ=255)
                  tttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:2402783/69‑1 (MQ=255)
                  tttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:2571172/69‑1 (MQ=255)
                  tttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:1851635/69‑1 (MQ=255)
                  tttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:1644172/69‑1 (MQ=255)
                  tttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:3015776/69‑1 (MQ=255)
                  tttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:314663/69‑1 (MQ=255)
                  tttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:1206036/69‑1 (MQ=255)
                  tttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:405804/69‑1 (MQ=255)
                  tttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:872637/69‑1 (MQ=255)
                  tttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:3360851/69‑1 (MQ=255)
                  tttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:574479/69‑1 (MQ=255)
                   ttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:2866731/68‑1 (MQ=255)
                   ttAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTTATCATCCTTATTTTATgcgc                                                <  1:1697202/68‑1 (MQ=255)
                                   tggtggGCCGTTATCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGtt                               >  1:1175021/1‑69 (MQ=255)
                                   tggtggGCCGTTATCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGtt                               >  1:3374522/1‑69 (MQ=255)
                                     gtggGCCGTTATCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGtttt                             >  1:3293002/1‑69 (MQ=255)
                                     gtggGCCGTTATCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGtttt                             >  1:623035/1‑69 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATgcgc                                                >  1:3363154/1‑40 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATgcgc                                                >  1:1033197/1‑40 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATgcgc                                                >  1:2099631/1‑40 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATgcgc                                                >  1:681929/1‑40 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATgcgc                                                >  1:516254/1‑40 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATgcgc                                                >  1:1854965/1‑40 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATgcgc                                                >  1:1609735/1‑40 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   >  1:2910555/1‑69 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   <  1:3154354/69‑1 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   >  1:699321/1‑69 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   >  1:451442/1‑69 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   >  1:2553947/1‑69 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   <  1:3072220/69‑1 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   >  1:1405816/1‑69 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   <  1:1587425/69‑1 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   <  1:1491274/69‑1 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   <  1:2157636/69‑1 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   <  1:2191265/69‑1 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   >  1:923121/1‑69 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   <  1:1210383/69‑1 (MQ=255)
                                               aTCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   <  1:2314975/69‑1 (MQ=255)
                                                tCGCTTTGAGATCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCt                   <  1:3276547/68‑1 (MQ=255)
                                                  gCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTAcc                                      >  1:3149795/1‑47 (MQ=255)
                                                  gCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGAt                >  1:2357136/1‑69 (MQ=255)
                                                  gCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGAt                >  1:1336871/1‑69 (MQ=255)
                                                  gCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGAt                >  1:766296/1‑69 (MQ=255)
                                                  gCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGAt                >  1:1966742/1‑69 (MQ=255)
                                                  gCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGAt                >  1:2862519/1‑69 (MQ=255)
                                                  gCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGAt                >  1:456138/1‑69 (MQ=255)
                                                  gCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGAt                >  1:592082/1‑69 (MQ=255)
                                                     ttGAGTTCATTCTTATCATCCTTATTTTATGCGCACTGATTGCCGCCCGttt                              >  1:2333319/1‑52 (MQ=255)
                                                     ttGAGTTCATTCTTATCATCCTTATTTTATGCGCACTGATTGCCGCCCGttt                              >  1:3344787/1‑52 (MQ=255)
                                                     ttGAGTTCATTCTTATCATCCTTATTTTATGCGCACTGATTGCCGCCCGttt                              >  1:1435124/1‑52 (MQ=255)
                                                     ttGAGTTCATTCTTATCATCCTTATTTTATGCGCACTGATTGCCGCCCGttt                              >  1:1472471/1‑52 (MQ=255)
                                                     ttGAGTTCATTCTTATCATCCTTATTTTATGCGCACTGATTGCCGCCCGttt                              >  1:1502991/1‑52 (MQ=255)
                                                     ttGAGTTCATTCTTATCATCCTTATTTTATGCGCACTGATTGCCGCCCGttt                              >  1:341546/1‑52 (MQ=255)
                                                     ttGAGTTCATTCTTATCATCCTTATTTTATGCGCACTGATTGCCGCCCGttt                              >  1:2340358/1‑52 (MQ=255)
                                                     ttGAGTTCATTCTTATCATCCTTATTTTATGCGCACTGATTGCCGCCCGttt                              >  1:2642799/1‑52 (MQ=255)
                                                     ttGAGTTCATTCTTATCATCCTTATTTTATGCGCACTGATTGCCGCCCGttt                              >  1:2661833/1‑52 (MQ=255)
                                                     ttGAGTTCATTCTTATCATCCTTATTTTATGCGCACTGATTGCCGCCCGttt                              >  1:1658037/1‑52 (MQ=255)
                                                     ttGAGTTCATTCTTATCATCCTTATTTTATGCGCACTGATTGCCGCCCGttt                              >  1:2893849/1‑52 (MQ=255)
                                                     ttGAGTTCATTCTTATCATCCTTATTTTATGCGCACTGATTGCCGCCCGttt                              >  1:2016790/1‑52 (MQ=255)
                                                     ttGAGTTCATTCTTATCATCCTTATTTTATGCGCACTGATTGCCGCCCGttt                              >  1:2960540/1‑52 (MQ=255)
                                                     ttGAGTTCATTCTTATCATCCTTATTTTATGCGCACTGATTGCCGCCCGtt                               >  1:3019825/1‑51 (MQ=255)
                                                     ttGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGt             <  1:2753875/69‑1 (MQ=255)
                                                     ttGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGt             <  1:2371277/69‑1 (MQ=255)
                                                     ttGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGt             <  1:1408487/69‑1 (MQ=255)
                                                          ttCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGtt         <  1:872087/68‑1 (MQ=255)
                                                          ttCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGtt         <  1:314203/68‑1 (MQ=255)
                                                          ttCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGtt         <  1:1394190/68‑1 (MQ=255)
                                                          ttCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGtt         <  1:2912793/68‑1 (MQ=255)
                                                          ttCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGtt         <  1:2261893/68‑1 (MQ=255)
                                                          ttCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGtt         <  1:1641916/68‑1 (MQ=255)
                                                          ttCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGtt         <  1:1528021/68‑1 (MQ=255)
                                                          ttCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGtt         <  1:785340/68‑1 (MQ=255)
                                                            cATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTAt       >  1:1985972/1‑68 (MQ=255)
                                                               tcagATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTg    <  1:1043205/65‑1 (MQ=255)
                                                               tCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTg    <  1:3436308/68‑1 (MQ=255)
                                                               tCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTg    <  1:3369522/68‑1 (MQ=255)
                                                               tCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTg    <  1:3134875/68‑1 (MQ=255)
                                                               tCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTg    <  1:3120433/68‑1 (MQ=255)
                                                               tCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTg    <  1:2837903/68‑1 (MQ=255)
                                                               tCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTg    <  1:655319/68‑1 (MQ=255)
                                                               tCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTg    <  1:2816986/68‑1 (MQ=255)
                                                               tCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTg    <  1:2594453/68‑1 (MQ=255)
                                                               tCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTg    <  1:2318775/68‑1 (MQ=255)
                                                               tCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTg    <  1:2047292/68‑1 (MQ=255)
                                                               tCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTg    <  1:1666620/68‑1 (MQ=255)
                                                               tCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTg    <  1:1227000/68‑1 (MQ=255)
                                                               tCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAATTATCTg    <  1:1460870/68‑1 (MQ=255)
                                                                cTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTg    <  1:645198/67‑1 (MQ=255)
                                                                cTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTGAt  >  1:2615872/1‑69 (MQ=255)
                                                                  |                                                                  
GTAACGTTTAGCACCGCCTTTAGCGGAGGGTAGTATGGTGGGCCGTTATCGCTTTGAGTTCATTCTGATCATCCTTATTTTATGCGCACTGATTACCGCCCGTTTTTATCTTTCCTGATTGTAGTTATCTGAT  >  minE/999434‑999566

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