BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	110,660	T→A	16.4%	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	16.4%	84.3 / 9.8	36	I173I (ATT→ATA)	USA300HOU_RS00515	putative lipoprotein
Reads supporting (aligned to +/- strand): ref base T (8/22); new base A (4/2); total (12/24)
Fisher's exact test for biased strand distribution p-value = 1.49e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.80e-01

TAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAAT  >  USA300TCH1516_ALE/110525‑110798

tAAAACGGTCGATAATAAAATCATTCCAAAAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCat                                                                                                                                        <  1:50430/140‑1 (MQ=255)

  aaaTGTTCGATAATAAAAACAGTACAACAAAAGAAATGAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTGTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCatat                                                                                                                                      <  1:21574/140‑1 (MQ=17)

  aaaTGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAATAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCatat                                                                                                                                      <  1:127216/140‑1 (MQ=255)

               taaAATCATTCCAACAAAAGAAATTAAAGATTAAAAAATAAAAAAAGAAATCTAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGc                                                                                                                         <  1:79705/140‑1 (MQ=255)

                  aaTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGa                                                                                                                      <  2:85610/140‑1 (MQ=255)

                    tCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGATTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGt                                                                                                                    <  1:180117/140‑1 (MQ=255)

                          caacaaAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATACAGAGGTGCCGAGTTATTCg                                                                                                              >  2:76317/1‑140 (MQ=255)

                              aaaaGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTa                                                                                                          <  1:166489/140‑1 (MQ=255)

                                          aGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                              <  1:136603/140‑1 (MQ=255)

                                          aGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                              >  1:266777/1‑140 (MQ=255)

                                            aTGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                            <  1:46506/140‑1 (MQ=255)

                                                     tAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATgatgat                                                                                   <  1:191782/140‑1 (MQ=255)

                                                               aaTCGAAAGCTTGAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                                         <  2:85319/140‑1 (MQ=255)

                                                                aTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaa                                                                        >  1:223588/1‑140 (MQ=255)

                                                                aTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTAGGATAAATATCAATTAACTAATGATGATTATAATGTaaa                                                                        >  1:78964/1‑140 (MQ=255)

                                                                aTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTCATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaa                                                                        >  2:149546/1‑140 (MQ=255)

                                                                     aaacgggaaGTTCTTTGTTCAATATGGCGACATTAAAAATTTGAAAGATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGACGAGTTATTCGGCTAAATATCAATTAACTGATGATGATGATAATGTAAAACAAt                                                                   >  2:251946/8‑140 (MQ=17)

                                                                       aCTTTAAGTGCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                 <  2:229416/140‑1 (MQ=255)

                                                                        cTTTAATTTTTTTTTTTAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTCCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAGGATGATTATAATGTAAAACAATTAc                                                                <  1:32335/140‑1 (MQ=17)

                                                                           tAAGTTCCTTGTTCAATATGGCGACTTTAAAAATTTGAAAAAGTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCa                                                             <  2:200253/140‑1 (MQ=255)

                                                                             aGTTCTTTGTTCAATATCGTGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                           <  1:165566/140‑1 (MQ=255)

                                                                             aGTGCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                           >  2:670/1‑140 (MQ=255)

                                                                                 cTTTGTTCAATATGGCTAAGTTAAAAATTTGAAAAATTATAAAGACGGAGATAATTCATAAAATGCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgat                                                       <  1:17448/140‑1 (MQ=17)

                                                                                                 gACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGCGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAg                                       <  2:237246/140‑1 (MQ=255)

                                                                                                        aaaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATAAGATATACCGACGAGTAAAGCt                                >  1:201318/1‑140 (MQ=255)

                                                                                                            tttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGAATATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCaa                            >  1:172859/8‑140 (MQ=14)

                                                                                                              tGAAAAATTATAAAGACTGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAg                          <  1:17414/140‑1 (MQ=255)

                                                                                                              tGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATAGCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAg                          <  1:59359/140‑1 (MQ=255)

                                                                                                                     ttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGt                   >  1:148638/1‑140 (MQ=255)

                                                                                                                     ttATAAAGAGGGAGATATATCATAGAAGCCAGAGGTGCCGAGTTATTCGGCTAAAGATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACGGACGAGTAAAGGTCCAAAGTTATTGt                   <  2:146434/140‑1 (MQ=17)

                                                                                                                      tataAAGATGGAGATATATCATATAATCCAGAAATGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACGGACGAGTAAAGCTCCAAAGATATTGtt                  >  2:60244/1‑140 (MQ=17)

                                                                                                                       ataAAGATGGAGATATATCATATAATCCATGTGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCCAAGTTATTGTTa                 >  2:161058/1‑140 (MQ=17)

                                                                                                                         aaaGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaa               <  1:217423/140‑1 (MQ=255)

                                                                                                                            gatggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAgg            <  1:11424/137‑1 (MQ=255)

                                                                                                                                   atatTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAggg     <  1:171829/140‑1 (MQ=255)

                                                                                                                                     atTGCATAGAATCCAGAGGTGCCGAGTTATCCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGaa   <  2:180962/140‑1 (MQ=255)

                                                                                                                                      tttCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAAt  <  2:266777/140‑1 (MQ=255)

TAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAAT  >  USA300TCH1516_ALE/110525‑110798

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`