BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,201,454	T→C	18.2%	V144A (GTT→GCT)	ileS →	Isoleucine‑‑tRNA ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,201,454	0	T	C	18.2%	44.4 / 6.5	22	V144A (GTT→GCT)	ileS	Isoleucine‑‑tRNA ligase
Reads supporting (aligned to +/- strand): ref base T (10/8); new base C (2/2); total (12/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.72e-01

GAACAAGCATTAACGAAAAAAGGTGTTGACCGAAAGAAAATGTCAACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAATGGCAGATAAAGGTTTAATTTATAAAGGTAAAAAGCCAGTTTATTGGTCTCCTTCAAGTGAGT  >  USA300TCH1516_ALE/1201327‑1201594

gAACAAGCATGAACGAAAAAAGGTGTTGACCGAAAGAAAATGTCCACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACttt                                                                                                                                 <  1:91429/141‑1 (MQ=255)

     aGCATTAACGAAAAAAGGTGTTGACCGAAAGAAAATGTCAACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGa                                                                                                                            >  1:72685/1‑141 (MQ=255)

      gCATTAACGAAAAAAGGTGTTGACCGAAAGAAAATGTCAACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGAt                                                                                                                           >  1:112507/1‑141 (MQ=255)

           aaCGAAAAAAGGTGTTGACCGAAAGAAAATGTCAACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGCTCGTGGTGACTTTAATGATCCata                                                                                                                      >  2:90539/1‑141 (MQ=255)

           aaCGAAAAAAGGTGTTGACCGAAAGAAAATGTCAACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGCTCGTGGTGACTTTAATGATCCata                                                                                                                      >  2:19351/1‑141 (MQ=255)

            aCGAAAAAAGGTGTTGACCGAAAGAAAATGTCAACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCatat                                                                                                                     <  1:134699/141‑1 (MQ=255)

                 aaaaGGTGTTGACCGAAAGAAAATGTCAACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTAc                                                                                                                >  2:191689/1‑141 (MQ=255)

                                  agaaaATGTCAACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACg                                                                                               >  1:129745/1‑141 (MQ=255)

                                      aaTGTCAACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGc                                                                                           >  1:219930/1‑141 (MQ=255)

                                       aTGTCAACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCt                                                                                          >  1:47444/1‑141 (MQ=255)

                                       aTGTCAACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCt                                                                                          <  1:94136/141‑1 (MQ=255)

                                            aaCAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGcaca                                                                                     >  2:4966/1‑141 (MQ=255)

                                                     aTTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTAt                                                                            >  2:31320/1‑141 (MQ=255)

                                                                 aTGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAAt                                                                <  2:135887/141‑1 (MQ=255)

                                                                 aTGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAAt                                                                <  2:148075/141‑1 (MQ=255)

                                                                   gTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGCTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAATgg                                                              <  1:90539/141‑1 (MQ=255)

                                                                   gTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGCTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAATgg                                                              <  1:19351/141‑1 (MQ=255)

                                                                        gAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAATGGCAGAt                                                         <  1:189719/141‑1 (MQ=255)

                                                                                                  aCAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAATGGCAGATAAAGGTTTAATTTATAAAGGTaaaaa                               >  1:19078/1‑141 (MQ=255)

                                                                                                                 tAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAATGGCAGATAAAGGTTTAATTTATAAAGGTAAAAAGCCAGTTTATTGGtc                <  2:72685/141‑1 (MQ=255)

                                                                                                                 tAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAATGGCAGATAAAGGTTTAATTTATAAAGGTAAAAAGCCAGTTTATTGGtc                <  1:163546/141‑1 (MQ=255)

                                                                                                                   gACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAATGGCAGATAAAGGTTTAATTTATAAAGGTAAAAAGCCAGTTTATTGGtctc              >  2:89438/1‑141 (MQ=255)

                                                                                                                               ttCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAATGGCAGATAAAGGTTTAATTTATAAAGGTAAAAAGCCAGTTTATTGGTCTCCTTCAAGTGAgg  >  2:25379/1‑140 (MQ=255)

                                                                                                                               ttCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAATGGCAGATAAAGGTTTAATTTATAAAGGTAAAAAGCCAGTTTATTGGTCTCCTTCAAGTGAGt  >  2:21192/1‑141 (MQ=255)

GAACAAGCATTAACGAAAAAAGGTGTTGACCGAAAGAAAATGTCAACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAATGGCAGATAAAGGTTTAATTTATAAAGGTAAAAAGCCAGTTTATTGGTCTCCTTCAAGTGAGT  >  USA300TCH1516_ALE/1201327‑1201594

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`