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 712,419 C→T 35.5% G339G (GGG→GGA)  pyrC ← dihydro‑orotase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE712,4190CT35.5% 60.5 / 50.0 87G339G (GGG→GGA) pyrCdihydro‑orotase
Reads supporting (aligned to +/- strand):  ref base C (23/33);  new base T (26/5);  total (49/38)
Fisher's exact test for biased strand distribution p-value = 1.14e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.83e-01

GTAAAATAACCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGTTG  >  minE/712353‑712478
                                                                  |                                                           
gTAAAATAACCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTcccc                                                           >  1:2495100/1‑69 (MQ=255)
gTAAAATAACCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTcccc                                                           >  1:2507705/1‑69 (MQ=255)
gTAAAATAACCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTcccc                                                           >  1:154891/1‑69 (MQ=255)
 tAAAATAACCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCg                                                          >  1:827215/1‑69 (MQ=255)
 tAAAATAACCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCg                                                          >  1:3111248/1‑69 (MQ=255)
 tAAAATAACCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCg                                                          >  1:1150256/1‑69 (MQ=255)
 tAAAATAACCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCg                                                          >  1:1221007/1‑69 (MQ=255)
 tAAAATAACCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCg                                                          >  1:2180597/1‑69 (MQ=255)
 tAAAATAACCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCg                                                          >  1:63649/1‑69 (MQ=255)
 tAAAATAACCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCg                                                          >  1:1637783/1‑69 (MQ=255)
       aaCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:1559871/69‑1 (MQ=255)
       aaCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:592064/69‑1 (MQ=255)
       aaCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:2286331/69‑1 (MQ=255)
       aaCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:2298448/69‑1 (MQ=255)
       aaCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:281394/69‑1 (MQ=255)
       aaCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:1553024/69‑1 (MQ=255)
       aaCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:1229498/69‑1 (MQ=255)
       aaCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:130345/69‑1 (MQ=255)
       aaCCTAATCACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGAGAgg                                                    <  1:2858582/69‑1 (MQ=255)
        aCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTccc                                                            >  1:3006988/1‑60 (MQ=255)
        aCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGa                                                   <  1:811427/69‑1 (MQ=255)
        aCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGa                                                   >  1:3027665/1‑69 (MQ=255)
        aCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGa                                                   >  1:310700/1‑69 (MQ=255)
        aCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGa                                                   >  1:3031687/1‑69 (MQ=255)
        aCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGa                                                   >  1:1321780/1‑69 (MQ=255)
        aCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGa                                                   <  1:1893386/69‑1 (MQ=255)
        aCCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGa                                                   >  1:1937625/1‑69 (MQ=255)
            aaTGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGAATgg                                               <  1:3131372/69‑1 (MQ=255)
            aaTGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGAATgg                                               <  1:3044277/69‑1 (MQ=255)
            aaTGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGAATgg                                               <  1:986120/69‑1 (MQ=255)
            aaTGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGAATgg                                               <  1:173448/69‑1 (MQ=255)
               gACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:2559627/61‑1 (MQ=255)
               gACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:2891030/61‑1 (MQ=255)
               gACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:586526/61‑1 (MQ=255)
               gACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:2993483/61‑1 (MQ=255)
               gACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:1616658/61‑1 (MQ=255)
               gACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:1258830/61‑1 (MQ=255)
               gACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    <  1:939786/61‑1 (MQ=255)
                    caGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAgg                                                    >  1:2442271/1‑56 (MQ=255)
                    caGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAg                                                     >  1:660411/1‑55 (MQ=255)
                    caGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGa                                                   >  1:1821835/1‑57 (MQ=255)
                    caGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGa                                                   >  1:1142597/1‑57 (MQ=255)
                    caGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGa                                                   >  1:3164147/1‑57 (MQ=255)
                    caGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGa                                                   >  1:2774519/1‑57 (MQ=255)
                    caGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGa                                                   >  1:2561701/1‑57 (MQ=255)
                    caGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGa                                                   >  1:1702328/1‑57 (MQ=255)
                    caGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGa                                                   >  1:362116/1‑57 (MQ=255)
                    caGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGa                                                   >  1:474382/1‑57 (MQ=255)
                    caGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGa                                                   >  1:478470/1‑57 (MQ=255)
                    caGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGa                                                   >  1:573843/1‑57 (MQ=255)
                         aGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAgg                                                    >  1:659520/1‑51 (MQ=255)
                            tACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGtcatca                               <  1:2059913/69‑1 (MQ=255)
                            tACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGtcatca                               <  1:1613270/69‑1 (MQ=255)
                            tACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGtcatca                               <  1:1279749/69‑1 (MQ=255)
                            tACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGtcatca                               <  1:1293159/69‑1 (MQ=255)
                            tACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGtcatca                               <  1:861115/69‑1 (MQ=255)
                            tACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGtcatca                               >  1:2756585/1‑69 (MQ=255)
                            tACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGtcatca                               >  1:2752508/1‑69 (MQ=255)
                             aCGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGtcatca                               >  1:677678/1‑68 (MQ=255)
                                     tATTGTTTAACGGACCAGGGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGc                       <  1:1953921/68‑1 (MQ=255)
                                     tATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGc                       <  1:671832/68‑1 (MQ=255)
                                     tATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGc                       <  1:1548370/68‑1 (MQ=255)
                                     tATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGc                       <  1:2486546/68‑1 (MQ=255)
                                     tATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGc                       <  1:1982603/68‑1 (MQ=255)
                                     tATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGc                       <  1:2049629/68‑1 (MQ=255)
                                              aCGGACCAGCGTACCGTTTCCCCGGCGAGGAATgg                                               <  1:3050137/35‑1 (MQ=255)
                                              aCGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTc              >  1:1551386/1‑68 (MQ=255)
                                              aCGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTc              >  1:2098487/1‑68 (MQ=255)
                                              aCGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTc              >  1:2881276/1‑68 (MQ=255)
                                              aCGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTc              >  1:915698/1‑68 (MQ=255)
                                              aCGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTc              >  1:3246039/1‑68 (MQ=255)
                                              aCGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTc              >  1:3346001/1‑68 (MQ=255)
                                              aCGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTc              >  1:865704/1‑68 (MQ=255)
                                                       cGTACCGTTTCTCCGGGGAGGAATGGCACCAGCGTCTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    >  1:1061122/1‑69 (MQ=255)
                                                       cGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    >  1:77216/1‑69 (MQ=255)
                                                       cGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    >  1:879039/1‑69 (MQ=255)
                                                       cGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    >  1:995736/1‑69 (MQ=255)
                                                       cGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    >  1:2881854/1‑69 (MQ=255)
                                                       cGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    >  1:2073347/1‑69 (MQ=255)
                                                       cGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    >  1:2030161/1‑69 (MQ=255)
                                                       cGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    >  1:1952087/1‑69 (MQ=255)
                                                       cGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    >  1:1795510/1‑69 (MQ=255)
                                                       cGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    >  1:167968/1‑69 (MQ=255)
                                                       cGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    >  1:1555636/1‑69 (MQ=255)
                                                       cGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    >  1:1462405/1‑69 (MQ=255)
                                                       cGTACCGTTTCTCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGAAGCTTTCAGCAACCTGt    >  1:2128131/1‑69 (MQ=255)
                                                       cGTACCGTTTCTCCGGCGAGGAATGGCACAAGCGTGTCATCAGTCAGTGCGATGCTTTCa             >  1:904537/1‑60 (MQ=255)
                                                       cGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    <  1:2425486/69‑1 (MQ=255)
                                                       cGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    <  1:2193283/69‑1 (MQ=255)
                                                       cGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGt    <  1:1120940/69‑1 (MQ=255)
                                                         tACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGTTg  <  1:2985162/69‑1 (MQ=255)
                                                                  |                                                           
GTAAAATAACCTAATGACAACAGGAAGCTACGATTTTTATTGTTTAACGGACCAGCGTACCGTTTCCCCGGCGAGGAATGGCACCAGCGTGTCATCAGTCAGTGCGATGCTTTCAGCAACCTGTTG  >  minE/712353‑712478

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