BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,468,907	A→T	18.5%	pseudogene (1802/2559 nt) pseudogene (1802/8622 nt)	ydbA → ydbA →	ECK1398:JW5802:b1401; predicted outer membrane protein, N‑ter fragment ECK1398:JW5802+JW1402:b4492; predicted outer membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,468,907	0	A	T	18.5%	58.3 / 9.0	27	pseudogene (1802/2559 nt) pseudogene (1802/8622 nt)	ydbA ydbA	ECK1398:JW5802:b1401; predicted outer membrane protein, N‑ter fragment ECK1398:JW5802+JW1402:b4492; predicted outer membrane protein
Reads supporting (aligned to +/- strand): ref base A (8/14); new base T (3/2); total (11/16)
Fisher's exact test for biased strand distribution p-value = 3.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.35e-01

TCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCACAACCAACAGTGGGAAGGTTTCGCTGG  >  W3110S.gb/1468837‑1468966

tCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTaa                                                             >  1:1097910/1‑71 (MQ=255)

  cGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACg                                                           >  1:681857/1‑71 (MQ=255)

       cTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAg                                                       >  1:1340269/1‑70 (MQ=255)

               aTTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGc                                                      <  1:1465349/63‑1 (MQ=255)

               aTTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGc                                              <  1:811414/71‑1 (MQ=255)

                  ggCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGa                                            >  1:881203/1‑70 (MQ=255)

                      tGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGAGACAggg                                       <  1:1057545/71‑1 (MQ=255)

                        cTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGtt                                     >  1:606615/1‑71 (MQ=255)

                           atcaACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCa                                   <  1:834254/70‑1 (MQ=255)

                           atcaACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCa                                   <  1:425666/70‑1 (MQ=255)

                            tcaACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGc                                              <  1:1676864/58‑1 (MQ=255)

                             caACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGAc                                           >  1:885471/1‑60 (MQ=255)

                              aaCGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACa                                          >  1:1441810/1‑60 (MQ=255)

                                cGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTATCGTTAg                                                       >  1:523863/1‑45 (MQ=255)

                                cGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTATCGTTAg                                                       >  1:525896/1‑45 (MQ=255)

                                      gggggCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCAcaacca                       <  1:125506/71‑1 (MQ=255)

                                        gggCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCAcaaccaac                     <  1:509128/71‑1 (MQ=255)

                                          gCAACAGTATCCAATACGGGTGATGTTATCGTTAGCAATGAAGCGACAGGGTTCAGCATcac                            <  1:531884/62‑1 (MQ=255)

                                          gCAACAGTATCCAATACGGGTGATGTTATCGTTAGCAATGAAGCGACAGGGTTCAGCATcac                            <  1:887690/62‑1 (MQ=255)

                                          gCAACAGTATCCAATACGGGTGATGTTAACGTTAGc                                                      <  1:893591/36‑1 (MQ=255)

                                           cAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCAcaaccaa                      <  1:1089922/67‑1 (MQ=255)

                                                  aTCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCAcaaccaa                      <  1:102951/60‑1 (MQ=255)

                                                         aCGGGTGATGTTATCGTTAGCAATGAAGCGACAGGGTTCAGCa                                >  1:1145262/1‑43 (MQ=255)

                                                               gATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCACAACCAACAGTGGGaa             >  1:1409255/1‑56 (MQ=255)

                                                                 tGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCACAACCAACAGTGGGaa             <  1:1603420/54‑1 (MQ=255)

                                                                 tGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCACAACCAACAGTGGGa              <  1:848553/53‑1 (MQ=255)

                                                                  gTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCACAACCAACAGTGGGAAGGTTTCGCTgg  >  1:615204/1‑64 (MQ=255)

                                                                   ttAACGTTAGCAATGAAGCGACAGGGTTCAGCATCACAACCAACAGTGGGAAGGt          <  1:1312802/55‑1 (MQ=255)

TCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTGATGTTAACGTTAGCAATGAAGCGACAGGGTTCAGCATCACAACCAACAGTGGGAAGGTTTCGCTGG  >  W3110S.gb/1468837‑1468966

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: `‑`