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 2,604,035 G→A 40.4% S212S (AGC→AGT)  yhiP ← predicted transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,604,0350GA40.4% 59.2 / 88.1 126S212S (AGC→AGT) yhiPpredicted transporter
Reads supporting (aligned to +/- strand):  ref base G (57/18);  new base A (23/28);  total (80/46)
Fisher's exact test for biased strand distribution p-value = 6.27e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01

Only 100 of 127 total aligned reads displayed.

TTGTGCATCAGCCATGCGCATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGT  >  minE/2603970‑2604102
                                                                 |                                                                   
ttGTGCATCAGCCATGCGCATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTg                                                                  <  1:434563/69‑1 (MQ=255)
ttGTGCATCAGCCATGCGCATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTg                                                                  <  1:1390075/69‑1 (MQ=255)
ttGTGCATCAGCCATGCGCATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTg                                                                  <  1:3106082/69‑1 (MQ=255)
       tCAGCCATGCGCATACGAAGATGATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCa                                                           >  1:3088695/1‑69 (MQ=255)
       tCAGCCATGCGCATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCa                                                           >  1:1703450/1‑69 (MQ=255)
       tCAGCCATGCGCATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCa                                                           >  1:2855968/1‑69 (MQ=255)
       tCAGCCATGCGCATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCa                                                           >  1:1630678/1‑69 (MQ=255)
       tCAGCCATGCGCATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCa                                                           >  1:2405246/1‑69 (MQ=255)
       tCAGCCATGCGCATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCa                                                           >  1:678679/1‑69 (MQ=255)
       tCAGCCATGCGCATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCa                                                           >  1:161263/1‑69 (MQ=255)
                cgcATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGa                                                  >  1:3349374/1‑69 (MQ=255)
                cgcATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGa                                                  >  1:3227864/1‑69 (MQ=255)
                cgcATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGa                                                  >  1:1545232/1‑69 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCTGCCGGaa                                                 <  1:27614/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:2536681/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:3390598/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:2000428/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:1804689/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:2027669/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:3230180/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:3050815/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:2815567/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:2877215/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:2462364/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:426705/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:811273/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:2770940/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:1311349/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:1452294/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:2635315/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:2782675/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:490707/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:1673443/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:1765088/69‑1 (MQ=255)
                 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                 <  1:1779084/69‑1 (MQ=255)
                      cGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTc                                                            >  1:308480/1‑53 (MQ=255)
                      cGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTc                                                            >  1:1200073/1‑53 (MQ=255)
                      cGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCgg                                            >  1:1650696/1‑69 (MQ=255)
                      cGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCgg                                            >  1:3096504/1‑69 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGACGCTCATCGGCCGGAAGTCggg                                           >  1:2494773/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAg                                                               >  1:3332698/1‑47 (MQ=38)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:2655294/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:2684238/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:2898475/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:2929505/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:3415106/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:512508/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:669173/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:74710/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:77133/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:884031/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:1363849/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:2036763/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:2560527/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:2031917/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:2003828/1‑67 (MQ=255)
                         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                           >  1:2329265/1‑67 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAg                                                >  1:2313551/1‑59 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      >  1:3177810/1‑69 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      <  1:2652171/69‑1 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      >  1:1981055/1‑69 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      <  1:3407919/69‑1 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      >  1:1839790/1‑69 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      <  1:343032/69‑1 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      >  1:525344/1‑69 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      >  1:529219/1‑69 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      <  1:588055/69‑1 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      <  1:592337/69‑1 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      >  1:1091199/1‑69 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      <  1:2058425/69‑1 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      >  1:3098701/1‑69 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      >  1:2062905/1‑69 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      >  1:1088840/1‑69 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      <  1:279910/69‑1 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      >  1:2441616/1‑69 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      <  1:2904647/69‑1 (MQ=255)
                            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      >  1:2230142/1‑69 (MQ=255)
                            tcaacaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                      >  1:3158687/1‑69 (MQ=255)
                             catcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCt                                                                   >  1:1866029/1‑39 (MQ=255)
                             catcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCt                                                                   >  1:1823670/1‑39 (MQ=255)
                             catcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCt                                                                   >  1:1562317/1‑39 (MQ=255)
                             catcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCt                                                                   >  1:3292250/1‑39 (MQ=255)
                                 accacGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAAcc                                  >  1:2136413/1‑68 (MQ=255)
                                 accacGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAAcc                                  >  1:1132375/1‑68 (MQ=255)
                                 accacGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAAcc                                  >  1:1833015/1‑68 (MQ=255)
                                 accacGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAAcc                                  >  1:1252040/1‑68 (MQ=255)
                                 accacGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAAcc                                  >  1:2639867/1‑68 (MQ=255)
                                            aaGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCAc                      <  1:2123575/69‑1 (MQ=255)
                                               tAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCa                    >  1:3012687/1‑68 (MQ=255)
                                               tAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCa                    >  1:2133343/1‑68 (MQ=255)
                                               tAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCAt                   >  1:3246523/1‑69 (MQ=255)
                                               tAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCAt                   >  1:611822/1‑69 (MQ=255)
                                               tAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCAt                   >  1:276671/1‑69 (MQ=255)
                                                aaCACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATg                              >  1:1605389/1‑57 (MQ=255)
                                                aaCACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCAt                   >  1:1612754/1‑68 (MQ=255)
                                                aaCACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCAt                   >  1:1184118/1‑68 (MQ=255)
                                                                tGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGt  <  1:771152/69‑1 (MQ=255)
                                                                tGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGt  <  1:405043/69‑1 (MQ=255)
                                                                tGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGt  <  1:881956/69‑1 (MQ=255)
                                                                 gCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGt  <  1:2499260/68‑1 (MQ=255)
                                                                 |                                                                   
TTGTGCATCAGCCATGCGCATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGT  >  minE/2603970‑2604102

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