Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	110,660	T→A	19.7%	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	19.7%	51.7 / 7.1	25	I173I (ATT→ATA)	USA300HOU_RS00515	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (8/12);  new base A (2/3);  total (10/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

AAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAA  >  USA300TCH1516_ALE/110527‑110797                                                                                                                                      |                                                                                                                                          aaaTGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCAtata                                                                                                                                    >  1:373799/1‑141 (MQ=255)   aTGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGACCACATTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAAt                                                                                                                                  >  1:199282/1‑141 (MQ=255)   aTGGTCGATAATAAAATCATGCCAACAAAAGAAATTAAAGATGAAAAAATAAAATAAGAAATCGAAAACTTTAAGTTCTGTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAAt                                                                                                                                  >  1:300873/1‑141 (MQ=255)       tctataatataatGATTCCAACAATACAAATTAAAGCTGAAAAAATAAAAAAATAAATCGAAAACTGTAAGTTCTTTGTGCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCag                                                                                                                              <  1:161338/138‑1 (MQ=17)                         caacaaAAGAAAGTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCgg                                                                                                            <  1:354611/141‑1 (MQ=255)                                  aaaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGATGCCGAGTTATTCGGCTAAATATc                                                                                                   >  1:42433/1‑141 (MQ=255)                                                acaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTCAAAAATTTGAAAAATTATAAAGACGGACATATTTCATATAAACCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                                     <  1:415593/139‑1 (MQ=255)                                                        aaaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCTGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATaa                                                                             <  1:308421/141‑1 (MQ=255)                                                         aaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAAt                                                                            <  1:164467/141‑1 (MQ=255)                                                         aaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAAATTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAGGAGGATTATaaa                                                                            >  1:154267/1‑140 (MQ=255)                                                                       cTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                              <  1:329152/141‑1 (MQ=255)                                                                          tAAGTTCTTTGCTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaa                                                           <  1:423405/141‑1 (MQ=255)                                                                                     ttCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgata                                                <  1:207690/141‑1 (MQ=255)                                                                                       cAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGAtata                                              >  1:350482/1‑141 (MQ=255)                                                                                       cAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGAgata                                              >  1:192176/1‑141 (MQ=255)                                                                                                               atgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGCGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTa                      <  1:94075/138‑1 (MQ=255)                                                                                                               aaaaaTTATAAAGACGGAGATATTTCATATCATCCAACGGTGCATAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTa                      <  1:240348/141‑1 (MQ=18)                                                                                                                 aaaTTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTAtt                    <  1:245780/141‑1 (MQ=255)                                                                                                                       aaaaGACGGAGATGTTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAATAGATATGATATACCGACGAGTAAAGCTCCCAAGTTATTGTTaaa              <  1:252927/140‑1 (MQ=255)                                                                                                                         aaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATATAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCAAAGGTTATTGTTAAAAg            >  1:312959/1‑141 (MQ=17)                                                                                                                          aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAgg           <  1:262238/141‑1 (MQ=255)                                                                                                                           gACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGt          <  1:174966/141‑1 (MQ=255)                                                                                                                             gagggaTATATCATATAATCAAGAGGTGCCGAATTATTCGGCTAAATAACAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTc        <  1:377372/137‑1 (MQ=17)                                                                                                                                agaTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAAAAATTACGCAAAAGATATGGTATACAGACGAGTAAAGCGCTAAAGTTATCGTTAAAAGGttaggg     >  1:151730/1‑137 (MQ=17)                                                                                                                                   tatTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGGTAAAAGGTTCAGGGaa  >  1:108027/1‑141 (MQ=255)                                                                                                                                      |                                                                                                                                          AAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAA  >  USA300TCH1516_ALE/110527‑110797

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑