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 1,255,821 C→T 31.7% H171Y (CAC→TAC)  yecE → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,255,8210CT31.7% 37.1 / 18.6 44H171Y (CAC→TAC) yecEconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (21/9);  new base T (3/11);  total (24/20)
Fisher's exact test for biased strand distribution p-value = 3.73e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.12e-01

ATTTTAGACAGCCGCCCGGTTCATGCAGCACGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTGACG  >  minE/1255785‑1255886
                                    |                                                                 
aTTTTAGACAGCCGCCCGGTTCATGCAGCACGTCCATACAGTGAAGCTATTCGCGACGCTCAACGaa                                     >  1:2805638/1‑67 (MQ=255)
aTTTTAGACAGCCGCCCGGTTCATGCAGCACGTCCATACAGTGAAGCTATTCGCGACGCTCAACGaa                                     >  1:284302/1‑67 (MQ=255)
aTTTTAGACAGCCGCCCGGTTCATGCAGCACGTCCATACAGTGAAGCTATTCGCGACGCTCAACGaa                                     >  1:1120842/1‑67 (MQ=255)
  tttAGACAGCCGCCCGGTTCATGCAGCACGTCCACACAGTGAAGCTATTCGCGACGCTCAACGaaaaaa                                 >  1:823288/1‑69 (MQ=255)
                  gTTCATGCAGCACGTCCATACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTa                 <  1:922038/69‑1 (MQ=255)
                  gTTCATGCAGCACGTCCATACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTa                 <  1:2623156/69‑1 (MQ=255)
                  gTTCATGCAGCACGTCCATACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTa                 <  1:192911/69‑1 (MQ=255)
                  gTTCATGCAGCACGTCCATACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTa                 <  1:1509143/69‑1 (MQ=255)
                  gTTCATGCAGCACGTCCATACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTa                 <  1:1422713/69‑1 (MQ=255)
                  gTTCATGCAGCACGTCCATACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTa                 <  1:1358633/69‑1 (MQ=255)
                  gTTCATGCAGCACGTCCATACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTa                 <  1:1343550/69‑1 (MQ=255)
                  gTTCATGCAGCACGTCCATACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTa                 <  1:310156/69‑1 (MQ=255)
                  gTTCATGCAGCACGTCCATACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTa                 <  1:596948/69‑1 (MQ=255)
                  gTTCATGCAGCACGTCCATACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTa                 <  1:108614/69‑1 (MQ=255)
                    tCATGCAGCACGTCCACACAGTGAAGCTATTCGCGAc                                               >  1:2980809/1‑37 (MQ=255)
                    tCATGCAGCACGTCCACACAGTGAAGCTATTCGCGAc                                               >  1:2927279/1‑37 (MQ=255)
                    tCATGCAGCACGTCCACACAGTGAAGCTATTCGCGAc                                               >  1:713361/1‑37 (MQ=255)
                    tCATGCAGCACGTCCACACAGTGAAGCTATTCGCGAc                                               >  1:1104228/1‑37 (MQ=255)
                    tCATGCAGCACGTCCACACAGTGAAGCTATTCGCGAc                                               >  1:2295474/1‑37 (MQ=255)
                    tCATGCAGCACGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACa               <  1:528423/69‑1 (MQ=255)
                    tCATGCAGCACGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACa               <  1:57606/69‑1 (MQ=255)
                    tCATGCAGCACGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACa               <  1:2692652/69‑1 (MQ=255)
                    tCATGCAGCACGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACa               <  1:1046643/69‑1 (MQ=255)
                    tCATGCAGCACGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACa               <  1:1857709/69‑1 (MQ=255)
                    tCATGCAGCACGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACa               <  1:1005922/69‑1 (MQ=255)
                    tCATGCAGCACGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACa               <  1:1066077/69‑1 (MQ=255)
                    tCATGCAGCACGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACa               <  1:2338978/69‑1 (MQ=255)
                    tCATGCAGCACGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACa               <  1:1978328/69‑1 (MQ=255)
                         cagcaCGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTg          >  1:2553131/1‑69 (MQ=255)
                         cagcaCGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTg          >  1:2142626/1‑69 (MQ=255)
                         cagcaCGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTg          >  1:717738/1‑69 (MQ=255)
                         cagcaCGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTg          >  1:1178598/1‑69 (MQ=255)
                         cagcaCGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTg          >  1:2113600/1‑69 (MQ=255)
                         cagcaCGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTg          >  1:2488770/1‑69 (MQ=255)
                         cagcaCGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTg          >  1:1238612/1‑69 (MQ=255)
                         cagcaCGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTg          >  1:487725/1‑69 (MQ=255)
                         cagcaCGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTg          >  1:3425591/1‑69 (MQ=255)
                         cagcaCGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTg          >  1:1300009/1‑69 (MQ=255)
                         cagcaCGTCCACACAGTGAAGCTATTCGCGACGCTC‑ACGAAAAAAACCTAAAGTTCCGGTACATGCTGt         >  1:2855127/1‑69 (MQ=255)
                          agcaCGTCCATACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTa                 <  1:1150582/61‑1 (MQ=255)
                              cGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTg     >  1:2378511/1‑69 (MQ=255)
                              cGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTg     >  1:3016109/1‑69 (MQ=255)
                              cGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTg     >  1:2731168/1‑69 (MQ=255)
                              cGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTg     >  1:2118275/1‑69 (MQ=255)
                                  cacacaGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTGACg  >  1:153383/1‑68 (MQ=255)
                                  cacacaGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTGACg  >  1:2943608/1‑68 (MQ=255)
                                  cacacaGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTGACg  >  1:3416978/1‑68 (MQ=255)
                                  cacacaGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTGACg  >  1:243716/1‑68 (MQ=255)
                                  cacacaGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTGACg  >  1:2927173/1‑68 (MQ=255)
                                  cacacaGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTGACg  >  1:515914/1‑68 (MQ=255)
                                  cacacaGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTGACg  >  1:2919954/1‑68 (MQ=255)
                                  cacacaGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTGACg  >  1:1218277/1‑68 (MQ=255)
                                  cacacaGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTGACg  >  1:2771723/1‑68 (MQ=255)
                                  cacacaGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTGACg  >  1:2393927/1‑68 (MQ=255)
                                  cacacaGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTGACg  >  1:833810/1‑68 (MQ=255)
                                  cacacaGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTGACg  >  1:2511451/1‑68 (MQ=255)
                                    |                                                                 
ATTTTAGACAGCCGCCCGGTTCATGCAGCACGTCCACACAGTGAAGCTATTCGCGACGCTCAACGAAAAAAACCTAAAGTTCCGGTACATGCTGTACTGACG  >  minE/1255785‑1255886

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