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 2,227,641 T→C 58.4% G238G (GGT→GGC)  yhdY → predicted amino‑acid transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,227,6410TC58.4% 31.8 / 60.6 84G238G (GGT→GGC) yhdYpredicted amino‑acid transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (20/15);  new base C (32/17);  total (52/32)
Fisher's exact test for biased strand distribution p-value = 4.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATTGATCCGCGCGCTGGTTGGCGTGATCCTGTTTCAGTCAGCATATGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGCTGGCGTTGGGTTACTGGAAA  >  minE/2227574‑2227707
                                                                   |                                                                  
aaTTGATCCGCGCGCTGGTTGGCGTGATCCTGTTTCAGTCAGCATATGTTGCGGAAGTCGTGCGAtgtg                                                                   <  1:2860956/69‑1 (MQ=255)
aaTTGATCCGCGCGCTGGTTGGCGTGATCCTGTTTCAGTCAGCATATGTTGCGGAAGTCGTGCGAGGTg                                                                   <  1:2968674/69‑1 (MQ=255)
aaTTGATCCGCGCGCTGGTTGGCGTGATCCTGTTTCAGTCAGCATATGTTGCGGAAGTCGTGCGAGGTg                                                                   <  1:2892124/69‑1 (MQ=255)
aaTTGATCCGCGCGCTGGTTGGCGTGATCCTGTTTCAGTCAGCATATGTTGCGGAAGTCGTGCGAGGTg                                                                   <  1:2447350/69‑1 (MQ=255)
aaTTGATCCGCGCGCTGGTTGGCGTGATCCTGTTTCAGTCAGCATATGTTGCGGAAGTCGTGCGAGGTg                                                                   <  1:2297972/69‑1 (MQ=255)
aaTTGATCCGCGCGCTGGTTGGCGTGATCCTGTTTCAGTCAGCATATGTTGCGGAAGTCGTGCGAGGTg                                                                   <  1:1337888/69‑1 (MQ=255)
aaTTGATCCGCGCGCTGGTTGGCGTGATCCTGTTTCAGTCAGCATATGTTGCGGAAGTCGTGCGAGGTg                                                                   <  1:1405403/69‑1 (MQ=255)
aaTTGATCCGCGCGCTGGTTGGCGTGATCCTGTTTCAGTCAGCATATGTTGCGGAAGGCGTGCGAGGTg                                                                   <  1:3318951/69‑1 (MQ=255)
aaTTGATCCGCGCGCTGGTTGGCGTGATACTGTTTCAGTCAGCATATGTTGCGGAAGTCGTGCGAGGTg                                                                   <  1:905640/69‑1 (MQ=255)
  ttGATCCGCGCGCTGGTTGGCGTGATCCTGTTTCAGTCAGCATATGTTGCGGAAGTCGTGCGAGGTgg                                                                  >  1:1595154/1‑68 (MQ=255)
                        tGATCCTGTTTCAGTCAGCATATGTTGCGGAAGTCGTGCGAGGTg                                                                   <  1:2095274/45‑1 (MQ=255)
                            ccTGTTTCAGTCAGCATATGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAat                                        >  1:1052251/1‑68 (MQ=255)
                            ccTGTTTCAGTCAGCATATGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAat                                        >  1:1107517/1‑68 (MQ=255)
                                  tcagtcagCATATGTTGCGGAAGTCGTGCGAGGCGGAtt                                                               >  1:961191/1‑39 (MQ=255)
                                  tcagtcagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAATATGAAg                                  >  1:3233764/1‑68 (MQ=255)
                                  tcagtcagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGc                                 >  1:312116/1‑69 (MQ=255)
                                  tcagtcagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGc                                 >  1:1669431/1‑69 (MQ=255)
                                  tcagtcagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGc                                 >  1:2877754/1‑69 (MQ=255)
                                  tcagtcagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGc                                 >  1:1306758/1‑69 (MQ=255)
                                  tcagtcagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGc                                 >  1:495281/1‑69 (MQ=255)
                                  tcagtcagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGc                                 >  1:455088/1‑69 (MQ=255)
                                  tcagtcagCATATGTTGCGGAAGTCGTGAGAGGCGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGc                                 >  1:315535/1‑69 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:865254/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:1071930/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:968957/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:3174609/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:261576/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:2570270/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:2556563/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:373068/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:1601762/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:1700076/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:560906/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:820692/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:1906702/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:2046102/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:1961790/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTa                                                 <  1:685550/48‑1 (MQ=255)
                                       cagCATATGTTGCGGAAGTCGTGCGAGCCGGATTACAGGCGCTGCCTa                                                 <  1:524321/48‑1 (MQ=39)
                                        agCATATGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCaga                           >  1:655194/1‑69 (MQ=255)
                                        agCATATGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCaga                           >  1:1329748/1‑69 (MQ=255)
                                        agCATATGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCaga                           >  1:3212869/1‑69 (MQ=255)
                                        agCATATGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCaga                           >  1:2547371/1‑69 (MQ=255)
                                        agCATATGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCaga                           >  1:124240/1‑69 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:478970/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:998270/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:3131585/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:777277/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:3397265/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:3028782/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:919088/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:2536267/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:1381350/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:1709375/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:1879100/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:1929928/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:2202474/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:2263883/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:1089399/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:2520651/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:2547497/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:2622025/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:2960402/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:2927102/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:2626120/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAata                                       >  1:2671105/1‑55 (MQ=255)
                                          cATATGTTGCGGAAGTCGTGCGAGGCGGATTACAGGCGCTGCCTAAAGGGCAat                                        >  1:2462161/1‑54 (MQ=255)
                                              tGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGc                      >  1:3300506/1‑68 (MQ=255)
                                              tGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGc                      >  1:1604052/1‑68 (MQ=255)
                                              tGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGc                      >  1:3037756/1‑68 (MQ=255)
                                              tGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGc                      >  1:958134/1‑68 (MQ=255)
                                              tGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGc                      >  1:1933610/1‑68 (MQ=255)
                                              tGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGc                      >  1:1114364/1‑68 (MQ=255)
                                              tGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGCt                     >  1:290988/1‑69 (MQ=255)
                                              tGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGCt                     >  1:761015/1‑69 (MQ=255)
                                              tGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGCt                     >  1:2546056/1‑69 (MQ=255)
                                                       aGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGCTGGCGTTgg             >  1:2785452/1‑68 (MQ=255)
                                                       aGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGCTGGCGTTgg             >  1:1041492/1‑68 (MQ=255)
                                                       aGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGCTGGCGTTgg             >  1:335485/1‑68 (MQ=255)
                                                        gTCGTGCGAGGTGGATTAAAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGCTGGCGTTGGGt           <  1:2979414/69‑1 (MQ=255)
                                                         tCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGCTGGCGTTGGGt           <  1:3167690/68‑1 (MQ=255)
                                                                 ggTGGATTACAGGGGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGCTGGCGTTGGGTTACTGGaaa  <  1:1420744/69‑1 (MQ=255)
                                                                 ggTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGCTGGCGTTGGGTTACTGGaaa  <  1:758196/69‑1 (MQ=255)
                                                                 ggTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGCTGGCGTTGGGTTACTGGaaa  <  1:2200871/69‑1 (MQ=255)
                                                                 ggTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGCTGGCGTTGGGTTACTGGaaa  <  1:2359509/69‑1 (MQ=255)
                                                                   |                                                                  
AATTGATCCGCGCGCTGGTTGGCGTGATCCTGTTTCAGTCAGCATATGTTGCGGAAGTCGTGCGAGGTGGATTACAGGCGCTGCCTAAAGGGCAATATGAAGCGGCAGAGTCGCTGGCGTTGGGTTACTGGAAA  >  minE/2227574‑2227707

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