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 2,397,994 C→T 34.0% F146F (TTC→TTT)  yigE → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,397,9940CT34.0% 64.2 / 43.3 82F146F (TTC→TTT) yigEhypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (31/23);  new base T (11/17);  total (42/40)
Fisher's exact test for biased strand distribution p-value = 1.63e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

GCGTGTTTTATGTCGCGGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGTTGATGGAAAACGGTGTAATT  >  minE/2397942‑2398060
                                                    |                                                                  
gcgTGTTTTATGTCGCGGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAgaga                                                    <  1:270208/69‑1 (MQ=255)
gcgTGTTTTATGTCGCGGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAgaga                                                    <  1:1960033/69‑1 (MQ=255)
gcgTGTTTTATGTCGCGGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAgaga                                                    <  1:488555/69‑1 (MQ=255)
gcgTGTTTTATGTCGCGGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAgaga                                                    <  1:2272922/69‑1 (MQ=255)
gcgTGTTTTATGTCGCGGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAgaga                                                    <  1:915113/69‑1 (MQ=255)
gcgTGTTTTATGTCGCGGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAgaga                                                    <  1:2695675/69‑1 (MQ=255)
          tGTCGCGGGAGATAAAGTCGGCATCTTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGc                                          >  1:2003831/1‑69 (MQ=255)
          tGTCGCGGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCa                                                             >  1:865481/1‑50 (MQ=255)
          tGTCGCGGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTg                                           >  1:1314287/1‑68 (MQ=255)
          tGTCGCGGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTg                                           >  1:2043004/1‑68 (MQ=255)
          tGTCGCGGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTg                                           >  1:399229/1‑68 (MQ=255)
          tGTCGCGGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTg                                           >  1:1728363/1‑68 (MQ=255)
          tGTCGCGGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGc                                          >  1:965192/1‑69 (MQ=255)
          tGTCGCGGGAGATAAAGTCGGCATCATTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGc                                          >  1:715002/1‑69 (MQ=255)
              gcgGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGt                                       <  1:565078/68‑1 (MQ=255)
                 ggAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGc                                     >  1:1705623/1‑67 (MQ=255)
                 ggAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCa                                    >  1:898672/1‑68 (MQ=255)
                    gaTAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGttt                                            >  1:302963/1‑57 (MQ=255)
                    gaTAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCa                                >  1:3011689/1‑69 (MQ=255)
                    gaTAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCa                                >  1:2260179/1‑69 (MQ=255)
                    gaTAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCa                                >  1:2826329/1‑69 (MQ=255)
                    gaTAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCa                                >  1:2496519/1‑69 (MQ=255)
                    gaTAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCa                                >  1:1933337/1‑69 (MQ=255)
                    gaTAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCa                                >  1:2743819/1‑69 (MQ=255)
                    gaTAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCa                                >  1:2610770/1‑69 (MQ=255)
                    gaTAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCa                                >  1:2112125/1‑69 (MQ=255)
                    gaTAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCa                                >  1:3352599/1‑69 (MQ=255)
                    gaTAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCa                                >  1:527067/1‑69 (MQ=255)
                    gaTAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCa                                >  1:1676366/1‑69 (MQ=255)
                    gaTAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCa                                >  1:1032662/1‑69 (MQ=255)
                       aaaGTCGGCATCGTTCGTCTGGATGCCTTTAAAACCa                                                             >  1:2709457/1‑37 (MQ=255)
                       aaaGTCGGCATCGTTCGTCTGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCa                                    >  1:346733/1‑62 (MQ=255)
                       aaaGTCGGCATCGTTCGTCTGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAgg                              >  1:3409722/1‑68 (MQ=255)
                       aaaGTCGGCATCGTTCGTCTGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAgg                              >  1:364778/1‑68 (MQ=255)
                       aaaGTCGGCATCGTTCGTCTGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAgg                              >  1:490204/1‑68 (MQ=255)
                       aaaGTCGGCATCGTTCGTCTGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAgg                              >  1:1647436/1‑68 (MQ=255)
                       aaaGTCGGCATCGTTCGTCTGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAgg                              >  1:2457406/1‑68 (MQ=255)
                       aaaGTCGGCATCGTTCGTCTGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAgg                              >  1:2746396/1‑68 (MQ=255)
                       aaaGTCGGCATCGTTCGTCTGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAgg                              >  1:158017/1‑68 (MQ=255)
                       aaaGTCGGCATCGTTCGTCTGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAgg                              >  1:768005/1‑68 (MQ=255)
                       aaaGTCGGCATCGTTCGTCTGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAgg                              >  1:1216724/1‑68 (MQ=255)
                       aaaGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAgg                              >  1:1061387/1‑68 (MQ=255)
                       aaaGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAgg                              >  1:816935/1‑68 (MQ=255)
                               cATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGtt                     <  1:361198/69‑1 (MQ=255)
                               cATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGtt                     <  1:2371751/69‑1 (MQ=255)
                               cATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGtt                     <  1:1491462/69‑1 (MQ=255)
                               cATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGtt                     <  1:296193/69‑1 (MQ=255)
                               cATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGtt                     <  1:2970313/69‑1 (MQ=255)
                               cATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGtt                     <  1:2268694/69‑1 (MQ=255)
                               cATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGtt                     <  1:3153618/69‑1 (MQ=255)
                               cATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGtt                     <  1:725990/69‑1 (MQ=255)
                                aTCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGtt                     <  1:2690534/68‑1 (MQ=255)
                                aTCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGtt                     <  1:2092001/68‑1 (MQ=255)
                                      cgtCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGTTGATGGaa              >  1:1775663/1‑69 (MQ=255)
                                      cgtCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGTTGATGGaa              >  1:749691/1‑69 (MQ=255)
                                      cgtCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGTTGATGGaa              >  1:14662/1‑69 (MQ=255)
                                      cgtCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGTTGATGGaa              >  1:131158/1‑69 (MQ=255)
                                        tCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGtt                     <  1:2874473/60‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCTGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:28397/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:1793563/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:1910040/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:1545792/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:812395/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:1474260/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:1355357/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:951068/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:976828/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:525958/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:1881863/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:1907743/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:2067463/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:3352962/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:3300415/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCATTGTTGATGGAAAACg          <  1:2518645/69‑1 (MQ=255)
                                          tGGATGCCTTTAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGCGCCATTGTTGATGGAAAACg          <  1:511055/69‑1 (MQ=255)
                                            gATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGTTGATGGAAAACgg         >  1:1666543/1‑68 (MQ=255)
                                              tGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGTTGATGGAAAACGgt        <  1:3373286/67‑1 (MQ=255)
                                              tGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGTTGATGGAAAACGgt        <  1:2227388/67‑1 (MQ=255)
                                              tGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGTTGATGGAAAACGgt        <  1:2481708/67‑1 (MQ=255)
                                                  ttCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGTTGATGGAAAACGGTGtaatt  <  1:547426/69‑1 (MQ=255)
                                                  ttCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGTTGATGGAAAACGGTGtaatt  <  1:2054289/69‑1 (MQ=255)
                                                  ttCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGTTGATGGAAAACGGTGtaatt  >  1:2082439/1‑69 (MQ=255)
                                                    |                                                                  
GCGTGTTTTATGTCGCGGGAGATAAAGTCGGCATCGTTCGTCTGGATGCCTTCAAAACCAGTAAAGAGATTCAGTTTGCGGTGCAGTCAGGGCCAATGTTGATGGAAAACGGTGTAATT  >  minE/2397942‑2398060

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