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 1,903,969 A→G 37.3% G651G (GGT→GGC)  ptr ← protease III

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,903,9690AG37.3% 44.6 / 51.8 83G651G (GGT→GGC) ptrprotease III
Reads supporting (aligned to +/- strand):  ref base A (20/32);  new base G (17/14);  total (37/46)
Fisher's exact test for biased strand distribution p-value = 1.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

TCATCTCGCGAGAAGTACGGCACTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGCTCAAGCTGATCTT  >  minE/1903901‑1904030
                                                                    |                                                             
tCATCTCGCGAGAAGTACGGCACTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTa                                                               <  1:912070/69‑1 (MQ=255)
                 cGGCACTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGaa                                                <  1:2970363/67‑1 (MQ=255)
                 cGGCACTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGaa                                                <  1:1029110/67‑1 (MQ=255)
                 cGGCACTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGaa                                                <  1:2542470/67‑1 (MQ=255)
                 cGGCACTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGaa                                                <  1:1114419/67‑1 (MQ=255)
                 cGGCACTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGaa                                                <  1:459583/67‑1 (MQ=255)
                 cGGCACTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGaa                                                <  1:1470548/67‑1 (MQ=255)
                 cGGCACTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATc                                              <  1:3184914/69‑1 (MQ=255)
                 cGGCACTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATc                                              <  1:1994412/69‑1 (MQ=255)
                 cGGCACTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATc                                              <  1:1568736/69‑1 (MQ=255)
                  ggCACTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGaa                                                <  1:2893662/66‑1 (MQ=255)
                  ggCACTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATc                                              <  1:1509090/68‑1 (MQ=255)
                      cTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCcatca                                         >  1:4859/1‑69 (MQ=255)
                           gagaGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTg                                     <  1:3133025/68‑1 (MQ=255)
                           gagaGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCCGAATCCATCATCTg                                     <  1:3110143/68‑1 (MQ=255)
                            agagCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGt                                   <  1:1015463/69‑1 (MQ=255)
                            agagCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGt                                   <  1:959510/69‑1 (MQ=255)
                            agagCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGt                                   <  1:530205/69‑1 (MQ=255)
                                           gCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCg                    <  1:180206/69‑1 (MQ=255)
                                           gCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCg                    <  1:1062901/69‑1 (MQ=255)
                                           gCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCg                    <  1:2271206/69‑1 (MQ=255)
                                           gCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCg                    <  1:434402/69‑1 (MQ=255)
                                            cATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCg                    <  1:1763401/68‑1 (MQ=255)
                                             aTAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCg                    <  1:2203056/67‑1 (MQ=255)
                                              tAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATcc                                             <  1:2308112/41‑1 (MQ=255)
                                              tAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATcc                                             <  1:3405212/41‑1 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCg                    <  1:1545299/64‑1 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCg                    <  1:2772931/64‑1 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCg                    <  1:1304634/64‑1 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCg                    <  1:274162/64‑1 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCt                 >  1:2226170/1‑67 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTg                >  1:1512778/1‑68 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTg                >  1:3346563/1‑68 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTg                >  1:3185546/1‑68 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTg                >  1:2760948/1‑68 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTg                >  1:963804/1‑68 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTg                >  1:3075653/1‑68 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTg                >  1:3373727/1‑68 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTg                >  1:1252691/1‑68 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTg                >  1:1831567/1‑68 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTg                >  1:1816622/1‑68 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTg                >  1:16953/1‑68 (MQ=255)
                                                aTCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTg                >  1:79260/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGa                         >  1:3182846/1‑58 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:3345080/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:3381594/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:462978/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:971477/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:660665/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:677301/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:777074/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:2935171/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:2003175/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:2056314/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:1518992/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:2095792/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:1457856/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:1257438/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:2805784/1‑68 (MQ=255)
                                                 tCGCCTGCTCAAACGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGc               >  1:1022183/1‑68 (MQ=255)
                                                       gCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGCTCAAGCt        <  1:3159703/69‑1 (MQ=255)
                                                       gCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGCTCAAGCt        <  1:2423897/69‑1 (MQ=255)
                                                       gCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGCTCAAGCt        <  1:2861961/69‑1 (MQ=255)
                                                       gCTCAAACGCTTTACCCTTTTCTGCGGAATACATCATCTGGTTATACCAGGACTTCGCCTGCTCAAGCt        <  1:705160/69‑1 (MQ=255)
                                                          cAAACGCTTTACACTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGCTCAAGCTGa      >  1:945305/1‑68 (MQ=255)
                                                             aCGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTtat                                <  1:109931/39‑1 (MQ=255)
                                                             aCGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTtat                                <  1:1472968/39‑1 (MQ=255)
                                                             aCGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTtat                                <  1:754288/39‑1 (MQ=255)
                                                             aCGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTtat                                <  1:1023351/39‑1 (MQ=255)
                                                             aCGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTtat                                <  1:3073357/39‑1 (MQ=255)
                                                             aCGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTtat                                <  1:1552230/39‑1 (MQ=255)
                                                             aCGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTtat                                <  1:556035/39‑1 (MQ=255)
                                                             aCGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTtat                                <  1:1556256/39‑1 (MQ=255)
                                                             aCGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTtat                                <  1:2206416/39‑1 (MQ=255)
                                                             aCGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTtat                                <  1:2350871/39‑1 (MQ=255)
                                                             aCGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTtat                                <  1:2519988/39‑1 (MQ=255)
                                                             aCGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTtat                                <  1:323480/39‑1 (MQ=255)
                                                             aCGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTtat                                <  1:2866117/39‑1 (MQ=255)
                                                             aCGCTTTGCCCTTTTCTGCGGAATCCATCATCTGGTtat                                <  1:2895506/39‑1 (MQ=255)
                                                             aCGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGCTCAAGCTGATCtt  >  1:1863044/1‑69 (MQ=255)
                                                             aCGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGCTCAAGCTGATCtt  >  1:2074962/1‑69 (MQ=255)
                                                             aCGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGCTCAAGCTGATCtt  >  1:3362491/1‑69 (MQ=255)
                                                             aCGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGCTCAAGCTGATCtt  >  1:2574092/1‑69 (MQ=255)
                                                             aCGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGCTCAAGCTGATCtt  >  1:2771237/1‑69 (MQ=255)
                                                                    |                                                             
TCATCTCGCGAGAAGTACGGCACTTGCGAGAGCATCTGCGCGGGCATAATCGCCTGCTCAAACGCTTTACCCTTTTCTGCGGAATCCATCATCTGGTTATACCAGGACTTCGCCTGCTCAAGCTGATCTT  >  minE/1903901‑1904030

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