Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	110,660	T→A	18.0%	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	18.0%	95.4 / 12.5	43	I173I (ATT→ATA)	USA300HOU_RS00515	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (18/17);  new base A (4/4);  total (22/21)
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

GTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGG  >  USA300TCH1516_ALE/110532‑110794                                                                                                                                 |                                                                                                                                       gTCGCTAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTATTCAATATGGCGACTTTAAAAATTCGAAAAATTATAAAGACGGAGATATATAATAAAATCCa                                                                                                                            >  2:370290/1‑141 (MQ=17)              tCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGtt                                                                                                               >  1:22875/1‑141 (MQ=255)                aTTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCAGAGTTAt                                                                                                             >  1:19202/1‑141 (MQ=255)                      acaaAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCAAGAGGTGCCGAGTTATTCggat                                                                                                       >  2:64351/1‑139 (MQ=255)                           aaaaaTTGAAAACGAAAAAATAAAAAACGAAGTCTAAATCTTTAAGTTCTTTTGTCAATATGGCGACGTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGATGCGCCTAGCTATTCGGCTAAata                                                                                                  <  2:262370/139‑1 (MQ=17)                           aGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                  <  2:19446/141‑1 (MQ=255)                           aGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                  <  1:380076/141‑1 (MQ=255)                                   aaGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGATTTATTCGGCTAAATATCAATTaa                                                                                          >  2:301382/1‑141 (MQ=255)                                   aaGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAAGTACCGAGTTATTCGGCTAAATATCAATTaa                                                                                          >  2:84638/1‑141 (MQ=255)                                           aaaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                                  <  2:22875/141‑1 (MQ=255)                                             aaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAtgatga                                                                                >  1:92207/1‑141 (MQ=255)                                                        aaaTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGTAGATATTTCATATTATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                                     <  2:41654/141‑1 (MQ=255)                                                        aaaTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGCTGATTATAATGTaa                                                                     <  1:249995/141‑1 (MQ=255)                                                          agcGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaaa                                                                   <  2:234301/139‑1 (MQ=255)                                                            cGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACa                                                                 <  1:100120/141‑1 (MQ=255)                                                                          tCTTGGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGATATTTTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgat                                                   <  1:336089/141‑1 (MQ=255)                                                                               gTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgat                                              >  2:41311/1‑141 (MQ=255)                                                                               gTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgaa                                              >  2:253894/1‑140 (MQ=255)                                                                               gTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCAAGAGGTGCCGAGTTATTCGGCTAAATATAAATTTACTAATGATGATTATAATGTAAAACAATTACGCAAAGgatatgat                                              >  2:103011/1‑141 (MQ=255)                                                                                         gCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacga                                    >  1:96324/1‑141 (MQ=255)                                                                                         gCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATAAGATATACcgacga                                    >  1:237991/1‑141 (MQ=255)                                                                                           gACTTTAAAAATTGTAAGAATTATAAAGACGGATATATTTCATATAATCCAGAGGTGGCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGGAAAACAATTACGCAAAAGATATGATATAACGAGGAGt                                  >  2:99031/1‑141 (MQ=17)                                                                                             cTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCACAGCAGAGGATATACCGACGAGTaa                                <  2:369273/141‑1 (MQ=18)                                                                                             cTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTaa                                <  1:210929/141‑1 (MQ=255)                                                                                              tttAAAAATTTGAACAATTATAAAGACGGAGATATTTCATATAATCCATAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATTTAAAACAATTACGCAAAAGATATGATATAACGACGAggaca                               >  1:168143/1‑137 (MQ=17)                                                                                               ttAAAAAATTGAAAAATTTGAATGTCGGGGATATTTTAGATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATTATTATAATGTAAAACAATTACGCAAAAGATATGAGATACCGACGAGTAAAg                              <  2:13188/141‑1 (MQ=17)                                                                                                  aaaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGGGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTc                           <  2:168143/141‑1 (MQ=255)                                                                                                   aaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATCATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTcc                          <  1:12742/141‑1 (MQ=255)                                                                                                    aaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCa                         <  2:14124/141‑1 (MQ=255)                                                                                                    aaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCa                         <  2:355220/141‑1 (MQ=255)                                                                                                      tttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCAGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCaaa                       >  2:247088/8‑141 (MQ=14)                                                                                                         aatgaaTTATAAAGATGGAGATATATCATATAATCCGGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGtt                    <  1:222108/137‑1 (MQ=17)                                                                                                            gaagtataAAGATGGATATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTAtt                 <  2:97702/137‑1 (MQ=255)                                                                                                            gaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATGAACTAATGATGATTATAATGTAAAACCATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTAtt                 <  2:190692/140‑1 (MQ=255)                                                                                                              aTTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGt               <  1:27131/141‑1 (MQ=255)                                                                                                               ttAAAAAGATGGAGATATATTATATAATCCAGAGGTGCCTAGTTCTTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGtt              <  2:174029/141‑1 (MQ=18)                                                                                                                  taAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCCATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCACAGTTATTGTTaaa           >  1:172145/1‑141 (MQ=255)                                                                                                                   aaaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaaa          >  1:63889/1‑141 (MQ=255)                                                                                                                   aaaGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTAaaaa          >  2:13001/1‑141 (MQ=255)                                                                                                                    aaGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGCCGAGTAAAGCTCCCAAGTTATTGTTAAAAg         >  2:358098/1‑141 (MQ=255)                                                                                                                        tggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTc     >  2:135466/2‑141 (MQ=255)                                                                                                                        cGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAATGGGttg     >  1:302121/1‑140 (MQ=255)                                                                                                                           agaTATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATGAATTAATTAATGATGATGATAATGTAAAACAATGACGCAAAAGATATGATATACCGAGGAGTAGAGCTCCAAAGTTATTGTTAAAAAGTTCAgg  >  2:31130/1‑141 (MQ=18)                                                                                                                                 |                                                                                                                                       GTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGG  >  USA300TCH1516_ALE/110532‑110794

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: ‑