Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,078,573	(T)7→8	coding (246/681 nt)	USA300HOU_RS10490 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,078,566	1	.	T	93.9%	107.9 / 1.0	33	coding (253/681 nt)	USA300HOU_RS10490	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base T (16/15);  total (17/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

TGACAAATGCATATGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTG‑TTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAGATTGCA  >  USA300TCH1516_ALE/2078431‑2078697                                                                                                                                         |                                                                                                                                      tGACAAATGCATATGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTG‑ttttttttgaca                                                                                                                           <  3:29016/148‑6 (MQ=255)           atatGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACt                                                                                                                <  4:401622/148‑1 (MQ=255)           atatGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACt                                                                                                                <  4:291975/148‑1 (MQ=255)            tatGGAGTGGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGAATATAAACTAATAACAAGCGTTCCAATTAATGTTATAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTc                                                                                                               <  4:78523/148‑1 (MQ=255)             atGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAATCTCa                                                                                                              <  4:40861/148‑1 (MQ=255)             atGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCa                                                                                                              <  4:23189/148‑1 (MQ=255)              tGCAGTTGACAAATAGATTGACTTTGGTTCGATCCCATCTGCTTCATAAGCCTATCAACTAATAACAAGCGTTCCAATTAATGTTTAAACCATGCCAGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAGACTCat                                                                                                             <  4:208302/148‑1 (MQ=255)              tGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTa                                                                                                                    >  1:64041/1‑141 (MQ=255)                   ttGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATaaa                                                                                                        >  3:146595/1‑148 (MQ=255)                   ttGAAAAATAGATTGAATATAGATCAATCACATATGCTTTATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAAGATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTACCCTAAtataca                                                                                                        >  4:288984/1‑146 (MQ=255)                         aaTAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATaa                                                                                                         >  1:5798/1‑141 (MQ=255)                          aTAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCACTTAATGTTAAACCAATGCATGTAATATAGTTGGCATTAAGCAATTG‑TTTTTTTTCGACACTGGTAAACTCATATAAAaataat                                                                                                  >  4:62366/1‑148 (MQ=255)                          aTAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAataata                                                                                                 >  4:325997/1‑148 (MQ=255)                                tGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATc                                                                                           >  3:410732/1‑148 (MQ=255)                                tGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATc                                                                                           <  4:111155/148‑1 (MQ=255)                                 gAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCa                                                                                          >  4:176835/1‑148 (MQ=255)                                  aaTTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCAt                                                                                         >  4:121951/1‑148 (MQ=255)                                               taaaTCTACTTAATAAGCAAATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTaccac                                                                                   <  1:18356/138‑1 (MQ=255)                                               cacaTCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCt                                                                            <  4:196375/148‑1 (MQ=255)                                               cacaTCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAACAATATGAATCATTACCACCTAATCt                                                                            >  4:100982/1‑148 (MQ=255)                                                             aaGCATATAAACTAATAACAAGCGTTCCAATAAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTTTaa                                                              >  4:331934/1‑148 (MQ=255)                                                                       aCTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGAcc                                                    >  3:98809/1‑148 (MQ=255)                                                                          aataaAAAGCGTTCCAATTAATATTAAAACAAAGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGc                                                 <  4:128974/148‑1 (MQ=255)                                                                                aaGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTaa                                           <  3:81689/148‑1 (MQ=255)                                                                                   cGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAAt                                        <  3:287666/148‑1 (MQ=255)                                                                                                         aTGCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGa                  <  4:250944/148‑1 (MQ=255)                                                                                                           gCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑TTTTTTTTTAAACTCATATAAAAATAATATGAATCATTACCATCTAATCTACGATTGAGTCTAAATAATTGACCAGCATCTAAAATCCAAATAATCAATATTGTTTGACt                >  4:117548/1‑148 (MQ=255)                                                                                                           gCATGTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATAttg                       >  2:42350/1‑141 (MQ=255)                                                                                                               gTAATATAGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTtata            >  3:21199/1‑148 (MQ=255)                                                                                                                   tataGTTGGCATTAAGCAATTGTTTTTTTT‑‑TTTTTTTTTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAg        >  4:274030/1‑148 (MQ=255)                                                                                                                   tataGTTGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAg        <  3:325997/148‑1 (MQ=255)                                                                                                                    ataGTTGGCATTAAGCAATTG‑TTTTTTTTCGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAg        <  3:62366/148‑1 (MQ=255)                                                                                                                         tGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAGATTGCa  <  3:176835/148‑1 (MQ=255)                                                                                                                         tGGCATTAAGCAATTGTTTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCAAAATAATCAATATTGTTGGACTTATAAAAGATTGCa  >  3:261429/1‑148 (MQ=255)                                                                                                                                         |                                                                                                                                      TGACAAATGCATATGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAATTG‑TTTTTTT‑‑GACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAGATTGCA  >  USA300TCH1516_ALE/2078431‑2078697

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑