Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	110,660	T→A	19.4%	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	19.4%	59.8 / 10.5	31	I173I (ATT→ATA)	USA300HOU_RS00515	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (10/15);  new base A (2/4);  total (12/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.81e-01

ATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGG  >  USA300TCH1516_ALE/110529‑110794                                                                                                                                    |                                                                                                                                       aaggTCGGTAATAAAATCAATCAAAAAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATaa                                                                                                                                <  2:311468/138‑1 (MQ=17)                aTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAg                                                                                                                 <  2:68663/140‑1 (MQ=255)                               gataTTAAAGATGAAAAAATAAAAAAAGAAATTGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                  <  2:50294/137‑1 (MQ=255)                                 aaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTGTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCTTATAATCAAAAGGTACGTAGTTATTATGCTGAAGATc                                                                                                >  2:33019/1‑140 (MQ=17)                                 aaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATc                                                                                                >  1:61781/1‑140 (MQ=255)                                  aTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAAAATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCAAGAGTTGCCAAGTTATTAGGCTAAATATCa                                                                                               >  1:125100/1‑140 (MQ=17)                                                         aGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATg                                                                        <  2:5511/140‑1 (MQ=255)                                                            aaTCGAATACGTAAAATTCTTTGTTCAATATAGCGAATTTAAAAATTTGAAAAATTATAAAGACGGAGACATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                                     <  1:33019/140‑1 (MQ=17)                                                             aTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaa                                                                    >  2:314129/1‑140 (MQ=255)                                                                  aaaCTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                               <  1:307677/140‑1 (MQ=255)                                                                  aaaCTTAAGCTTCTTTGGTTAATATTGTGTCTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCTGAGGTGCCGAGTGATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                               <  1:206704/140‑1 (MQ=17)                                                                      tttAAGTTCTTTGTTCAATATGGCGCCTTTAAAAATTTGAAAAATTATAAAGACGGAGACATTTTATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                           <  2:346678/140‑1 (MQ=255)                                                                                  gTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatga                                               <  1:303657/140‑1 (MQ=255)                                                                                   ttCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgat                                              >  2:273341/1‑140 (MQ=255)                                                                                       atatGGCGACTTTAAAAATTTGCAACATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAc                                          >  2:176380/1‑140 (MQ=255)                                                                                            gCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTGTAATGTAAAACAATTACTCAAAAGATATGATATACcgacg                                     >  2:219723/1‑140 (MQ=255)                                                                                                  ttAAAGATTTAATGAATTAAAAAGATGGAAAAAAATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTaaa                               <  1:330760/140‑1 (MQ=11)                                                                                                   tAAAGATTTAATGAATTATAAAGATGGAGATATAGCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAg                              <  2:167995/140‑1 (MQ=11)                                                                                                    aaaaaTTTGAAAAATAATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATCATATACCGACGAGTAAAGc                             >  1:263818/1‑140 (MQ=255)                                                                                                    aaaaaTTTGAAAAATAATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATAATATACCGACGAGTAAAGc                             >  1:263817/1‑140 (MQ=255)                                                                                                         tttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCaa                        <  2:256725/133‑1 (MQ=255)                                                                                                              aaaaTTATAAAGACGGATATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTa                   <  2:323380/140‑1 (MQ=255)                                                                                                                aaTTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTCACTAATGATGATTATAATGTAAAACAATTACGCAAATGATATGATATACCGACGAGTAAAGCTCCAAAGTTAtt                 <  2:265793/140‑1 (MQ=255)                                                                                                                   tataAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGtt              <  2:318950/140‑1 (MQ=255)                                                                                                                     taAAGACGAAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaa            <  2:149034/140‑1 (MQ=255)                                                                                                                      aaaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaa           <  2:343423/140‑1 (MQ=255)                                                                                                                        aGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAg         >  2:66921/1‑140 (MQ=255)                                                                                                                          aCGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGt       <  2:170300/140‑1 (MQ=255)                                                                                                                           tggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAATATATGATATACCGACGAGTAAAGCTACGAAGTTATTGTTAAAAGGtt      >  2:300632/2‑140 (MQ=17)                                                                                                                              agaTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAg   >  1:331753/1‑140 (MQ=255)                                                                                                                               gaTATTTCATATAATCCAGAGGTTCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAgg  <  1:164033/140‑1 (MQ=255)                                                                                                                                    |                                                                                                                                       ATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGG  >  USA300TCH1516_ALE/110529‑110794

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: ‑