BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,934,773	T→A	13.0%	K159* (AAA→TAA)	USA300HOU_RS09605 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,934,773	0	T	A	13.0%	109.7 / 7.5	37	K159* (AAA→TAA)	USA300HOU_RS09605	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (17/15); new base A (3/2); total (20/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGTCAGAAAAATATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATAA  >  USA300TCH1516_ALE/1934635‑1934913

cTGTCAGAAAAATATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATAtttttt                                                                                                                                            >  2:146361/1‑141 (MQ=255)

       aaaaaTATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAAtt                                                                                                                                     >  1:94310/1‑141 (MQ=255)

        aaaaTATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTc                                                                                                                                    >  1:138762/1‑141 (MQ=255)

          aaTATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGTAATTTaa                                                                                                                                  >  1:538255/1‑141 (MQ=255)

             ataAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTATTTGAATTTCaaaaa                                                                                                                               <  1:57076/141‑3 (MQ=255)

              taAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCaaataa                                                                                                                              <  2:184189/141‑1 (MQ=255)

                aGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCaaataaat                                                                                                                            >  2:307929/1‑141 (MQ=255)

                aGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCaaataaat                                                                                                                            <  1:105735/141‑1 (MQ=255)

                    tCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTATTTGAATTTCAAAAAAATATTc                                                                                                                        <  1:436983/141‑1 (MQ=255)

                       atatTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAAGATTCttt                                                                                                                     <  1:510698/141‑1 (MQ=255)

                          ttAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCg                                                                                                                  <  1:258931/141‑1 (MQ=255)

                            aaTTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTa                                                                                                                <  2:327046/141‑1 (MQ=255)

                                tCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTAtttt                                                                                                            <  2:203891/141‑1 (MQ=255)

                                            tCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCATACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAAAGAATATTTTTTTGAAATTCAAATATATATTTTTTGCGTATTTTGATTTCATCttt                                                                                                >  1:351686/1‑140 (MQ=255)

                                              aTAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATc                                                                                              <  1:256895/141‑1 (MQ=255)

                                                   tttCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTaaaa                                                                                         >  1:205093/1‑141 (MQ=255)

                                                        cTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCa                                                                                    >  1:329940/1‑141 (MQ=255)

                                                           aaGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCAttt                                                                                 <  1:778463/141‑1 (MQ=255)

                                                            aGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGAAAGTTACACACGAGATAGTGTTTAGTAGAAATGCTAATAAATTGGCTGTGCGTATTTTGAGTTCATCTTATCTAAAATATCAtttt                                                                                >  2:114104/1‑141 (MQ=255)

                                                            aGTATTTTTTCTTTTCTTCAAACTCTTCATCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCAtttt                                                                                <  1:87217/141‑1 (MQ=255)

                                                             gTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTc                                                                               <  1:240679/141‑1 (MQ=255)

                                                                          tcttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAGATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCtttt                                                                  <  1:198341/141‑1 (MQ=255)

                                                                           cttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTa                                                                 >  1:227349/1‑141 (MQ=255)

                                                                            ttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTaa                                                                >  1:648590/1‑141 (MQ=255)

                                                                            ttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTaa                                                                >  1:256126/1‑141 (MQ=255)

                                                                               aaaCTCTTCTTTCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTc                                                             <  1:38418/141‑1 (MQ=255)

                                                                                     ttcttcCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAg                                                       >  1:502394/1‑141 (MQ=255)

                                                                                         tcCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGatat                                                   <  2:175950/141‑1 (MQ=255)

                                                                                              ttCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAat                                              >  1:229874/1‑141 (MQ=255)

                                                                                              ttCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTCTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAat                                              <  1:620967/141‑1 (MQ=255)

                                                                                                           ttGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTa                                 >  1:57332/1‑141 (MQ=255)

                                                                                                                       tCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTa                     >  1:57152/1‑141 (MQ=255)

                                                                                                                       tCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTa                     >  2:9653/1‑141 (MQ=255)

                                                                                                                        cTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTaa                    <  1:358663/141‑1 (MQ=255)

                                                                                                                           aaTTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAg                 >  2:132108/1‑141 (MQ=255)

                                                                                                                            cgcaaagaATATTTATTTGAATTTCAAAAAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGa                >  2:239931/6‑141 (MQ=39)

                                                                                                                             ttAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGaa               >  2:119657/1‑141 (MQ=255)

                                                                                                                                   aaTATTTATTTGAATTTCAAAAAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCt         >  1:448999/1‑141 (MQ=255)

                                                                                                                                          ttttGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATaa  <  1:702976/141‑1 (MQ=255)

CTGTCAGAAAAATATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATAA  >  USA300TCH1516_ALE/1934635‑1934913

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`