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 269,904 A→G 56.7% intergenic (‑92/‑114) xseB ← / → thiI exonuclease VII small subunit/sulfurtransferase required for thiamine and 4‑thiouridine biosynthesis

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE269,9040AG56.7% 56.3 / 130.9 169intergenic (‑92/‑114)xseB/thiIexonuclease VII small subunit/sulfurtransferase required for thiamine and 4‑thiouridine biosynthesis
Reads supporting (aligned to +/- strand):  ref base A (25/48);  new base G (46/49);  total (71/98)
Fisher's exact test for biased strand distribution p-value = 8.31e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01

Only 100 of 174 total aligned reads displayed.

CCGTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGGCTGCTGTATTT  >  minE/269844‑269971
                                                            |                                                                   
ccGTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCGCAGCaaa                                                              >  1:2791763/1‑68 (MQ=255)
ccGTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCGCAGCaaa                                                              >  1:2569789/1‑68 (MQ=255)
ccGTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCGCAGCaaa                                                              >  1:311102/1‑68 (MQ=255)
ccGTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCGCAGCaaa                                                              >  1:715782/1‑68 (MQ=255)
ccGTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCGCAGCaaa                                                              >  1:1826151/1‑68 (MQ=255)
ccGTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCGCAGCaaa                                                              >  1:3244438/1‑68 (MQ=255)
ccGTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCGCAGCaaa                                                              >  1:3367812/1‑68 (MQ=255)
ccGTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCGCAGCaaa                                                              >  1:1290271/1‑68 (MQ=255)
ccGTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCGCAGCaaa                                                              >  1:1339476/1‑68 (MQ=255)
ccGTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCGCAGCaaa                                                              >  1:562027/1‑68 (MQ=255)
ccGTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCGCAGCaa                                                               >  1:1019116/1‑67 (MQ=255)
  gTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCg                                                           <  1:3070466/69‑1 (MQ=255)
  gTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCg                                                           <  1:2086179/69‑1 (MQ=255)
  gTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCg                                                           <  1:2086035/69‑1 (MQ=255)
  gTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCg                                                           <  1:2941142/69‑1 (MQ=255)
       ggTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGt                                                       <  1:2419409/68‑1 (MQ=255)
       ggTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGt                                                       <  1:62329/68‑1 (MQ=255)
       ggTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGt                                                       <  1:2273156/68‑1 (MQ=255)
       ggTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGt                                                       <  1:693679/68‑1 (MQ=255)
       ggTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGt                                                       <  1:191118/68‑1 (MQ=255)
       ggTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGt                                                       <  1:2201582/68‑1 (MQ=255)
       ggTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGt                                                       <  1:2622896/68‑1 (MQ=255)
       ggTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGt                                                       <  1:262447/68‑1 (MQ=255)
                     ggCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGGGATGTTAGTGGTATACTTc                                         <  1:648465/68‑1 (MQ=255)
                     ggCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTc                                         <  1:2386589/68‑1 (MQ=255)
                       caaatagcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTgg                                                 >  1:3017064/1‑58 (MQ=255)
                       caaatagcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTgg                                                 >  1:53763/1‑58 (MQ=255)
                       caaatagcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTgg                                                 >  1:2218482/1‑58 (MQ=255)
                       caaatagcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTgg                                                 >  1:3123396/1‑58 (MQ=255)
                       caaatagcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTgg                                                 >  1:586883/1‑58 (MQ=255)
                       caaatagcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTgg                                                 >  1:468957/1‑58 (MQ=255)
                       caaatagcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTgg                                                 >  1:1556711/1‑58 (MQ=255)
                       caaatagcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTgg                                                 >  1:3268841/1‑58 (MQ=255)
                       aaaatagcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTgg                                                 >  1:2379785/2‑58 (MQ=255)
                         aatagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCgcgc                                    <  1:2164335/69‑1 (MQ=255)
                         aatagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCgcgc                                    <  1:2936629/69‑1 (MQ=255)
                         aatagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCgcgc                                    <  1:2971294/69‑1 (MQ=255)
                         aatagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCgcgc                                    <  1:2441766/69‑1 (MQ=255)
                         aatagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCgcgc                                    <  1:3248539/69‑1 (MQ=255)
                         aatagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCgcgc                                    <  1:309825/69‑1 (MQ=255)
                         aatagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCgcgc                                    <  1:2022896/69‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:3027375/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:3258689/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:34083/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:3004849/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:81060/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:346475/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:3139964/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:788818/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:2869361/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:1034125/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:218501/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:1508537/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:2709252/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:2685547/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:2655430/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:1114967/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:1588748/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:2091274/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:242974/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:1632425/57‑1 (MQ=255)
                          atagcaaataACGCGCAATGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCgcgc                                    <  1:1733506/68‑1 (MQ=255)
                            agcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTg                                 <  1:2992584/69‑1 (MQ=255)
                            agcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTg                                 <  1:2265105/69‑1 (MQ=255)
                            agcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTg                                 <  1:1207679/69‑1 (MQ=255)
                            agcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTg                                 <  1:338020/69‑1 (MQ=255)
                            agcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTg                                 <  1:408456/69‑1 (MQ=255)
                            agcaaataACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTg                                 <  1:1479610/69‑1 (MQ=255)
                                   aaCGCGCAATGTTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCgcgc                                    <  1:1234755/59‑1 (MQ=255)
                                    aCGCGCAATGGTAAGGTGATGTGCTCAGCAAAGCGATGTTAGTGGta                                               <  1:1228095/47‑1 (MQ=255)
                                          aaTGGTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGta                                               <  1:3435329/41‑1 (MQ=255)
                                          aaTGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAgg                   <  1:1533046/69‑1 (MQ=255)
                                          aaTGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAgg                   <  1:1125171/69‑1 (MQ=255)
                                          aaTGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAgg                   <  1:3435912/69‑1 (MQ=255)
                                          aaTGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAgg                   <  1:2543801/69‑1 (MQ=255)
                                           aTGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAgg                   <  1:2813075/68‑1 (MQ=255)
                                             ggTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACt                                           >  1:3033957/1‑42 (MQ=255)
                                             ggTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGgtgt                >  1:3129344/1‑69 (MQ=255)
                                             ggTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGgtgt                >  1:3062482/1‑69 (MQ=255)
                                             ggTAAGGTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGgtgt                >  1:23218/1‑69 (MQ=255)
                                                aaGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTggg             >  1:666716/1‑69 (MQ=255)
                                                aaGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTggg             >  1:716635/1‑69 (MQ=255)
                                                aaGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTggg             >  1:831711/1‑69 (MQ=255)
                                                  ggTGATGTGCGCAGCAAAGCGATGTTAGTGGTATAc                                            >  1:1906012/1‑36 (MQ=255)
                                                  ggTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTc                                         >  1:2487903/1‑39 (MQ=255)
                                                  ggTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGgc            >  1:163363/1‑68 (MQ=255)
                                                  ggTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGgc            >  1:1075564/1‑68 (MQ=255)
                                                  ggTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGgc            >  1:794319/1‑68 (MQ=255)
                                                  ggTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGgc            >  1:1368173/1‑68 (MQ=255)
                                                  ggTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGgc            >  1:924530/1‑68 (MQ=255)
                                                  ggTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGgc            >  1:3359512/1‑68 (MQ=255)
                                                  ggTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGgc            >  1:1676004/1‑68 (MQ=255)
                                                  ggTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGgc            >  1:2604222/1‑68 (MQ=255)
                                                  ggTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGgc            >  1:276271/1‑68 (MQ=255)
                                                  ggTGATGTGCGCAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGgc            >  1:2721972/1‑68 (MQ=255)
                                                         tgCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGGCTGCTGTAt    >  1:1544028/1‑69 (MQ=255)
                                                         tgCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGGCTGCTGTAt    >  1:2297383/1‑69 (MQ=255)
                                                           cacaGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGGCTGCTGTAttt  >  1:968421/1‑69 (MQ=255)
                                                           cacaGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGGCTGCTGTAttt  >  1:1434271/1‑69 (MQ=255)
                                                           cacaGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGGCTGCTGTAttt  >  1:2734052/1‑69 (MQ=255)
                                                            |                                                                   
CCGTCATGGTAACGGACTCAGGGCAAATAGCAAATAACGCGCAATGGTAAGGTGATGTGCACAGCAAAGCGATGTTAGTGGTATACTTCCGCGCCTGGATGCAGCCGCAGGTGTGGGCTGCTGTATTT  >  minE/269844‑269971

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A