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 961,630 T→A 44.8% T365S (ACA→TCA)  yddB ← predicted porin protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE961,6300TA44.8% 22.4 / 96.3 87T365S (ACA→TCA) yddBpredicted porin protein
Reads supporting (aligned to +/- strand):  ref base T (39/9);  new base A (15/24);  total (54/33)
Fisher's exact test for biased strand distribution p-value = 5.63e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGTTTTGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCATGATCGTGACGGGTATAAT  >  minE/961562‑961692
                                                                    |                                                              
tgtTTTGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGt                                                                >  1:3158411/1‑69 (MQ=255)
tgtTTTGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGt                                                                <  1:1869463/69‑1 (MQ=255)
tgtTTTGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGt                                                                <  1:1896102/69‑1 (MQ=255)
tgtTTTGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGt                                                                <  1:3418091/69‑1 (MQ=255)
tgtTTTGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGt                                                                <  1:1981277/69‑1 (MQ=255)
tgtTTTGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGt                                                                >  1:3372471/1‑69 (MQ=255)
tgtTTTGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGt                                                                <  1:3132813/69‑1 (MQ=255)
tgtTTTGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGt                                                                >  1:2507547/1‑69 (MQ=255)
tgtTTTGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGt                                                                <  1:3011681/69‑1 (MQ=255)
tgtTTTGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGt                                                                <  1:838157/69‑1 (MQ=255)
tgtTTTGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGt                                                                <  1:2754859/69‑1 (MQ=255)
tgtTTTGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGt                                                                <  1:969687/69‑1 (MQ=255)
    ttGAATGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAat                                                             >  1:1448267/1‑68 (MQ=255)
    ttGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAat                                                             >  1:244764/1‑68 (MQ=255)
    ttGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAat                                                             <  1:1319924/68‑1 (MQ=255)
    ttGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAat                                                             >  1:589257/1‑68 (MQ=255)
    ttGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAat                                                             >  1:3422644/1‑68 (MQ=255)
            gtAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCata                                                    >  1:2784146/1‑69 (MQ=255)
            gtAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCata                                                    >  1:2702076/1‑69 (MQ=255)
            gtAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCata                                                    >  1:1175121/1‑69 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATg                                                  >  1:120359/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATg                                                  >  1:2286769/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATg                                                  >  1:3264078/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:1690930/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:3096498/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:3140124/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:1301709/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:2329813/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:2096491/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:1992259/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:598070/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:197599/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:3428883/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:191491/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:470535/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:1074571/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:400374/1‑68 (MQ=255)
               aTTATCTACAGCCTGGGAAATGTGGCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATg                                                  >  1:3235773/1‑68 (MQ=255)
                  aTCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTAc                                               >  1:1360049/1‑68 (MQ=255)
                  aTCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTAc                                               >  1:2847046/1‑68 (MQ=255)
                     tACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACAt                                             >  1:589588/1‑67 (MQ=255)
                     tACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACAt                                             >  1:2708853/1‑67 (MQ=255)
                     tACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACAt                                             >  1:1842661/1‑67 (MQ=255)
                     tACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACAt                                             >  1:2258440/1‑67 (MQ=255)
                       cAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGaaa                                         >  1:70900/1‑69 (MQ=255)
                             gggAAATGTGTCCTAATCCG‑CACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGgt                                  <  1:762304/69‑1 (MQ=255)
                                aaaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAATTTCGgt                                  <  1:436378/67‑1 (MQ=255)
                                aaaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAATTTCGgt                                  <  1:8298/67‑1 (MQ=255)
                                aaaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGgt                                  <  1:2862066/67‑1 (MQ=255)
                                aaaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGgt                                  <  1:3076545/67‑1 (MQ=255)
                                aaaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGgt                                  <  1:483490/67‑1 (MQ=255)
                                aaaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGgt                                  <  1:439011/67‑1 (MQ=255)
                                aaaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGgt                                  <  1:1038963/67‑1 (MQ=255)
                                aaaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGgt                                  <  1:1978169/67‑1 (MQ=255)
                                aaaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGgt                                  <  1:1165455/67‑1 (MQ=255)
                                aaaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGgt                                  <  1:2505149/67‑1 (MQ=255)
                                 aaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTa                               <  1:1590839/69‑1 (MQ=255)
                                 aaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTa                               <  1:2716837/69‑1 (MQ=255)
                                 aaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTa                               <  1:1960823/69‑1 (MQ=255)
                                 aaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTa                               <  1:847742/69‑1 (MQ=255)
                                 aaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTa                               <  1:2648204/69‑1 (MQ=255)
                                 aaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGgt                                  <  1:2373028/66‑1 (MQ=255)
                                 aaTGTGTCCTAATCCGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGgt                                  <  1:2875552/66‑1 (MQ=255)
                                       tcatAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGAt                         >  1:152870/4‑69 (MQ=255)
                                       tCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGa                          >  1:1444891/1‑68 (MQ=255)
                                       tCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGa                          >  1:2069584/1‑68 (MQ=255)
                                       tCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGa                          >  1:2653830/1‑68 (MQ=255)
                                       tCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGAt                         >  1:2422761/1‑69 (MQ=255)
                                       tCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGAt                         >  1:728064/1‑69 (MQ=255)
                                       tCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGAt                         >  1:1244820/1‑69 (MQ=255)
                                       tCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGAt                         >  1:646341/1‑69 (MQ=255)
                                       tCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGAt                         >  1:616218/1‑69 (MQ=255)
                                       tCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGAt                         >  1:1949876/1‑69 (MQ=255)
                                       tCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGAt                         >  1:1513970/1‑69 (MQ=255)
                                       tCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGAt                         >  1:1004867/1‑69 (MQ=255)
                                              ccGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCAt                    <  1:785707/67‑1 (MQ=255)
                                              ccGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCAt                    <  1:927281/67‑1 (MQ=255)
                                              ccGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCAt                    <  1:2828812/67‑1 (MQ=255)
                                              ccGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCAt                    <  1:1733119/67‑1 (MQ=255)
                                              ccGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCAt                    <  1:289990/67‑1 (MQ=255)
                                              ccGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCAt                    <  1:294417/67‑1 (MQ=255)
                                              ccGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCAt                    <  1:3157421/67‑1 (MQ=255)
                                              ccGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCAt                    <  1:1772984/67‑1 (MQ=255)
                                              ccGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCAt                    <  1:2370043/67‑1 (MQ=255)
                                              ccGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCAt                    <  1:3296466/67‑1 (MQ=255)
                                              ccGCCACGGGTGCAACGCCCTGAAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCAt                    <  1:2367631/67‑1 (MQ=255)
                                                      ggTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCg                                    >  1:99230/1‑43 (MQ=255)
                                                      ggTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCATGATCGTGACg          >  1:1113177/1‑69 (MQ=255)
                                                      ggTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCATGATCGTGACg          >  1:2785003/1‑69 (MQ=255)
                                                            aCGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCATGATCGTGACGGGtat     <  1:550597/68‑1 (MQ=255)
                                                            aCGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCATGATCGTGACGGGtat     <  1:3023854/68‑1 (MQ=255)
                                                            aCGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCATGATCGTGACGGGtat     <  1:1142706/68‑1 (MQ=255)
                                                              gCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCATGATCGTGACGGGTATAAt  >  1:2095637/1‑69 (MQ=255)
                                                              gCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCATGATCGTGACGGGTATAAt  >  1:689346/1‑69 (MQ=255)
                                                              gCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCATGATCGTGACGGGTATAAt  >  1:361670/1‑69 (MQ=255)
                                                              gCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCATGATCGTGACGGGTATAAt  >  1:2402188/1‑69 (MQ=255)
                                                              gCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCATGATCGTGACGGGTATAAt  >  1:540403/1‑69 (MQ=255)
                                                              gCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCATGATCGTGACGGGTATAAt  >  1:166211/1‑69 (MQ=255)
                                                              gCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCATGATAGTGACGGGTATAAt  >  1:1536834/1‑69 (MQ=255)
                                                                    |                                                              
TGTTTTGAAGGTGTAATTATCTACAGCCTGGGAAATGTGTCCTAATCCGCCACGGGTGCAACGCCCTGTAATATCACCATATGTACATGAAAGTTCGGTGTACCAGATGTCATGATCGTGACGGGTATAAT  >  minE/961562‑961692

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