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 1,528,303 T→C 47.0% Y430H (TAT→CAT)  trmC → fused 5‑methylaminomethyl‑2‑thiouridine forming enzyme methyltransferase and FAD‑dependent demodification enzyme

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,528,3030TC47.0% 5.0 / 88.4 100Y430H (TAT→CAT) trmCfused 5‑methylaminomethyl‑2‑thiouridine forming enzyme methyltransferase and FAD‑dependent demodification enzyme
Reads supporting (aligned to +/- strand):  ref base T (32/21);  new base C (18/29);  total (50/50)
Fisher's exact test for biased strand distribution p-value = 4.46e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.23e-02

CAGCAGAACTGACCCGTAATGTGCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGCAGGAG  >  minE/1528238‑1528360
                                                                 |                                                         
cagcagAACTGACCCGTAATGTGCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATc                                                        <  1:710814/69‑1 (MQ=255)
    agAACTGACCCGTAATGTGCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGt                                                     >  1:1774189/1‑68 (MQ=255)
    agAACTGACCCGTAATGTGCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGt                                                     >  1:714566/1‑68 (MQ=255)
    agAACTGACCCGTAATGTGCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGt                                                     >  1:1474408/1‑68 (MQ=255)
    agAACTGACCCGTAATGTGCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGt                                                     >  1:328500/1‑68 (MQ=255)
    agAACTGACCCGTAATGTGCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGt                                                     >  1:799877/1‑68 (MQ=255)
             ccGTAATGTGCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAAttt                                           <  1:828729/69‑1 (MQ=255)
             ccGTAATGTGCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAAttt                                           <  1:845198/69‑1 (MQ=255)
                  aTGTGCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATcc                                       >  1:2250005/1‑68 (MQ=255)
                  aTGTGCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATcc                                       >  1:2159017/1‑68 (MQ=255)
                  aTGTGCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATcc                                       >  1:1992707/1‑68 (MQ=255)
                    gtgCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAAttt                                           <  1:1579323/62‑1 (MQ=255)
                     tgCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTa                                   >  1:3250972/1‑69 (MQ=255)
                     tgCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTa                                   >  1:681536/1‑69 (MQ=255)
                     tgCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTa                                   >  1:1542790/1‑69 (MQ=255)
                     tgCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTa                                   >  1:2177990/1‑69 (MQ=255)
                     tgCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTa                                   >  1:526431/1‑69 (MQ=255)
                     tgCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTa                                   >  1:107992/1‑69 (MQ=255)
                     tgCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTa                                   >  1:1078002/1‑69 (MQ=255)
                     tgCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTa                                   >  1:2269083/1‑69 (MQ=255)
                       cTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAg                                 <  1:259559/69‑1 (MQ=255)
                       cTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAg                                 <  1:2481142/69‑1 (MQ=255)
                       cTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAg                                 <  1:1032090/69‑1 (MQ=255)
                       cTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAg                                 <  1:1445778/69‑1 (MQ=255)
                       cTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAg                                 <  1:1118764/69‑1 (MQ=255)
                       cTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAg                                 <  1:2743004/69‑1 (MQ=255)
                                  tcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:1749269/68‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGTATGACGgttg                      <  1:49674/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:3183701/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:460367/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:351291/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:3385901/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:2523679/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:3293616/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:2549034/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:3155835/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:668802/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:2777374/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:684119/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:2721915/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:1016132/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:857359/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:1396556/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:1364319/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:850927/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:1561268/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:829287/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:170733/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:1120028/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:1092342/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:729583/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:88168/69‑1 (MQ=255)
                                  gcAACAGCAGGGTTTGCAGATTCATTATCAACATCACTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:1840711/69‑1 (MQ=255)
                                   cAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:1614018/68‑1 (MQ=255)
                                   cAACAGCAGGGTTTGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGgttg                      <  1:2944819/68‑1 (MQ=255)
                                             gTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAAtt           >  1:2253574/1‑69 (MQ=255)
                                              tttGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTgttggt                    >  1:3058894/1‑59 (MQ=255)
                                              tttGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGaa             >  1:234649/1‑66 (MQ=255)
                                              tttGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAAttt          >  1:3055663/1‑69 (MQ=255)
                                              tttGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAAttt          >  1:55845/1‑69 (MQ=255)
                                              tttGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAAttt          >  1:1041320/1‑69 (MQ=255)
                                              tttGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAAttt          >  1:14288/1‑69 (MQ=255)
                                              tttGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAAttt          >  1:2805720/1‑69 (MQ=255)
                                              tttGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAAttt          >  1:2687867/1‑69 (MQ=255)
                                              tttGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAAttt          >  1:1752284/1‑69 (MQ=255)
                                              tttGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAAttt          >  1:2134056/1‑69 (MQ=255)
                                              tttGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAAttt          >  1:2153109/1‑69 (MQ=255)
                                              tttGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAAtt           >  1:1125315/1‑68 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:671871/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:593478/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:674221/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:829882/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:500811/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:2726260/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:2595780/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:1020790/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:1308462/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:1334801/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:1785630/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:1797580/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:2050544/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:2535958/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:3016364/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:449307/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:3146655/1‑63 (MQ=255)
                                                tGCAGATTCATTATCAACATCAGTTACAGGATTTATCCCGTAAGGATGACGGTTGGTTGTTGa              >  1:3269554/1‑63 (MQ=255)
                                                  cAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGc       >  1:17011/1‑68 (MQ=255)
                                                   aGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGc       >  1:68141/1‑67 (MQ=255)
                                                   aGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGc       >  1:3426675/1‑67 (MQ=255)
                                                      tttATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGCAGgag  <  1:771285/69‑1 (MQ=255)
                                                      tttATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGCAGgag  <  1:1266579/69‑1 (MQ=255)
                                                      tttATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGCAGgag  <  1:526412/69‑1 (MQ=255)
                                                      tttATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGCAGgag  <  1:1696796/69‑1 (MQ=255)
                                                      tttATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGCAGgag  <  1:3242739/69‑1 (MQ=255)
                                                      tttATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGCAGgag  <  1:3139708/69‑1 (MQ=255)
                                                      tttATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGCAGgag  <  1:603113/69‑1 (MQ=255)
                                                      tttATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGCAGgag  <  1:45265/69‑1 (MQ=255)
                                                      tttATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGCAGgag  <  1:2988506/69‑1 (MQ=255)
                                                      tttATTATCAATATCAGTTAAAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGCAGgag  <  1:676237/69‑1 (MQ=255)
                                                      tttATTATCAATATCAGATACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGCAGgag  <  1:2503105/69‑1 (MQ=255)
                                                                 |                                                         
CAGCAGAACTGACCCGTAATGTGCTGGAACTGGCGCAACAGCAGGGTTTGCAGATTTATTATCAATATCAGTTACAGAATTTATCCCGTAAGGATGACTGTTGGTTGTTGAATTTTGCAGGAG  >  minE/1528238‑1528360

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