BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	110,660	T→A	10.5%	I173I (ATT→ATA)	USA300HOU_RS00515 →	putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	110,660	0	T	A	10.5%	106.4 / 4.2	38	I173I (ATT→ATA)	USA300HOU_RS00515	putative lipoprotein
Reads supporting (aligned to +/- strand): ref base T (11/23); new base A (2/2); total (13/25)
Fisher's exact test for biased strand distribution p-value = 5.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

CGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGA  >  USA300TCH1516_ALE/110521‑110796

cGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAACTTATAACGACGGGGATAttt                                                                                                                                         <  2:343300/141‑1 (MQ=255)

            tCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCag                                                                                                                             <  2:172621/141‑1 (MQ=255)

             cGATAATAACATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGCAAAATTATAAAGACGGAGATATTTCATATAATCCaga                                                                                                                            <  1:92609/141‑1 (MQ=255)

               ataataAAATCATTCCAACAAAAAAAAATAAAAAAAAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAgg                                                                                                                          <  2:318708/141‑1 (MQ=17)

                taataaAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAAATATTTCATATAATCCAGAGGt                                                                                                                         >  1:202576/1‑141 (MQ=255)

                   taaAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGcc                                                                                                                      <  2:83021/141‑1 (MQ=255)

                        tCATACCAACAAAAGTAAATAAAGATGAAAAAATAAAAAAAGAAATCGAATACTTTAATTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGtt                                                                                                                 <  2:225949/141‑1 (MQ=17)

                               aacaaAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGc                                                                                                          <  2:11166/141‑1 (MQ=255)

                                    aaGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                     <  2:62649/141‑1 (MQ=255)

                                     aGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                    <  1:14883/141‑1 (MQ=255)

                                     aGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                    <  2:232311/141‑1 (MQ=255)

                                        aaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTGGAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCAAGAGGTGCCGAGTTATTCGGCTAAATATCa                                                                                                 >  1:150405/1‑141 (MQ=255)

                                         aTTAAAGATAAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCaa                                                                                                <  2:182417/141‑1 (MQ=255)

                                            aaaGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCAAGAGGTGCCGAGTTATTCGGCTAAATATCAATTa                                                                                             >  2:131132/1‑141 (MQ=255)

                                             aataTGAAAAAATAAAAAAAGGAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGAGATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                            <  2:98367/138‑1 (MQ=255)

                                                   aaaaaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatt                                                                                      >  2:346497/1‑140 (MQ=255)

                                                              aaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAAt                                                                           <  1:272351/141‑1 (MQ=255)

                                                                  aaaTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                                       >  1:132358/1‑141 (MQ=255)

                                                                  aaaTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                                       <  1:295174/141‑1 (MQ=255)

                                                                      cGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACa                                                                   <  1:159303/141‑1 (MQ=255)

                                                                       gAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAaaaaaa                                                                  >  2:293572/1‑141 (MQ=255)

                                                                               tAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaa                                                          <  1:325150/141‑1 (MQ=255)

                                                                                          ttCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgata                                               <  2:83698/141‑1 (MQ=255)

                                                                                          ttCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgata                                               <  2:57084/141‑1 (MQ=255)

                                                                                            cAATATGGCGACTTTAAAACTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGAtata                                             >  1:182016/1‑141 (MQ=255)

                                                                                            cAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGAtata                                             <  1:47187/141‑1 (MQ=255)

                                                                                            cAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGAtata                                             >  1:31956/1‑141 (MQ=255)

                                                                                               tatGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATTATGTGAAATAATGACGCAAAAGATATGATATACcg                                          <  1:81982/141‑1 (MQ=255)

                                                                                                  ggCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacg                                       >  2:137363/1‑141 (MQ=255)

                                                                                                           aaaaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAACACAAGTACGCAAAAGATATGAGATACAGACGAGCAAAGCt                              >  2:208226/1‑141 (MQ=17)

                                                                                                              aaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATGCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCa                           <  1:144693/141‑1 (MQ=255)

                                                                                                               aTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAACGCTCCaa                          >  1:16681/1‑141 (MQ=255)

                                                                                                                        aTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTCATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGt                 <  2:176052/141‑1 (MQ=255)

                                                                                                                              aaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAg           >  1:237895/1‑141 (MQ=255)

                                                                                                                                 aCGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGtt        <  2:57469/141‑1 (MQ=255)

                                                                                                                                   ggAGATAGAGCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATGAACTAAGGGTGATGAGAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAGGGTTCa      >  2:105051/1‑141 (MQ=17)

                                                                                                                                     agaTATTGCAGATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATCATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAgg    <  1:202759/141‑1 (MQ=255)

                                                                                                                                     agaTAGTGCATATAATCCAGAGGTGCCGGGTGATTCGGCTAAATACCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATAGTATATACCCACGAGTAAAGCTCCAAAGTTATTGTTAAACGGTTccgt    <  2:42003/141‑4 (MQ=17)

                                                                                                                                      gaTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAggg   <  1:180730/141‑1 (MQ=255)

                                                                                                                                       atatatCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGa  <  1:301847/141‑1 (MQ=255)

CGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGA  >  USA300TCH1516_ALE/110521‑110796

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`