Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,857,867	C→T	7.9%	L169L (TTG→TTA)	USA300HOU_RS09235 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,857,867	0	C	T	7.9%	188.9 / 2.5	76	L169L (TTG→TTA)	USA300HOU_RS09235	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (32/37);  new base T (2/5);  total (34/42)
Fisher's exact test for biased strand distribution p-value = 4.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTTAGCTTCTTGAATCTCTTGTG  >  USA300TCH1516_ALE/1857728‑1858006                                                                                                                                            |                                                                                                                                             ttttttttACCGCTGCTTGTTGTGCTTTCAATGCCACTGTTTTTGGTTCTTCATTTTTTATAGCTGCACTTTTATCTTTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCa                                                                                                                                             <  2:378800/137‑1 (MQ=17) cttcttTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTTTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCa                                                                                                                                             <  2:63017/141‑1 (MQ=255) cttcttTTATCGCTGCTTGTTGTGCTATCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCAGCTTGAGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGTCTCTTGTGATGTATCACTCa                                                                                                                                             <  1:468061/141‑1 (MQ=255)   tcttTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCaaa                                                                                                                                           <  1:630128/141‑1 (MQ=255)        tATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAattatt                                                                                                                                      >  1:435498/1‑141 (MQ=255)        tATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCGTATGATGTttcattcaggttagt                                                                                                                                      >  2:178234/1‑134 (MQ=17)              tgctTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACt                                                                                                                                <  1:146107/141‑1 (MQ=255)                tttgttgTGCCTTCAATGCCCCTGCTTTTGGTTCTTCATTTGATTCTGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTCAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTg                                                                                                                              <  2:492310/140‑1 (MQ=25)                  tgttgtGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCTTCTTGTGATGTATCACTCAAATTATTTGCACTTGct                                                                                                                            >  2:295273/1‑141 (MQ=255)                       tgCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGcttcttc                                                                                                                       <  1:370140/141‑1 (MQ=255)                         ttttCAGTGCCACTGTTTTTGGTTTTGCATTTGTTTGTGCTGCGCTTTTGTCTTTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGcttcttc‑tt                                                                                                                    <  2:137864/140‑1 (MQ=17)                            tCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTTCTTTTTC‑TTTTa                                                                                                                 >  2:523532/1‑141 (MQ=255)                            tCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑ttttt                                                                                                                 >  2:313379/1‑140 (MQ=255)                            tCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTa                                                                                                                 >  1:376700/1‑141 (MQ=255)                             cAATGCCGCTGCTTTTGGTTATTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACATGCTTCTTC‑TTTTAt                                                                                                                >  1:480277/1‑141 (MQ=255)                             cAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTAt                                                                                                                >  1:424260/1‑141 (MQ=255)                               aTGCCACTGCTTTTGGTTCTTCATTTGCTACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAACTTATTTGCACTTGCTTCTTC‑TTTTATCg                                                                                                              <  1:301045/141‑1 (MQ=255)                               aTGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCg                                                                                                              >  1:55661/1‑141 (MQ=255)                                   cACTGCTTTTGGTTCTTCATTTGATATGACTTCTCGTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCgctgc                                                                                                          >  1:372262/1‑141 (MQ=17)                                       tcTTTTGCTTCTTCATCTTTTGTTGATGCATTTTTATCTTTCTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCttgt                                                                                                      <  2:372807/140‑1 (MQ=14)                                           ttGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTtgtg                                                                                                  >  1:314932/1‑141 (MQ=255)                                               ttcttcATTTGGTACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTTAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCttt                                                                                              <  2:625659/141‑1 (MQ=255)                                                         gATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGTTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGATTTTAAttctcct                                                                                    >  2:108757/1‑135 (MQ=17)                                                         gATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGCATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGcccag                                                                                    >  2:108771/1‑138 (MQ=255)                                                         gATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACt                                                                                    >  1:236271/1‑141 (MQ=255)                                                            aCAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTCATCGCTGCTTGCTGTGCCTTCAATGCCCCtccc                                                                                 >  2:508689/1‑138 (MQ=17)                                                            aCAGCTGCACTTTTATCTGTCTCTGCTTGTGCTTCTTTTTTAGCATCTTGAATCTCTTGTGCCTCTTGTGATTTATGAATCTACGCACTTGCACTTGCCTCTTC‑TTTCATCGCTATTTGTTGTGCTTTCGATTCCAGTGCt                                                                                 >  2:421899/1‑141 (MQ=14)                                                              aGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGAttt                                                                               >  1:300029/1‑141 (MQ=255)                                                               gctgtgcTTTTGTCTCTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGCATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCtttt                                                                              <  1:348173/135‑1 (MQ=14)                                                               gCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCtttt                                                                              >  1:759692/1‑141 (MQ=255)                                                               gCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCtttt                                                                              <  1:591257/141‑1 (MQ=255)                                                               gCTGCACTATTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCtttt                                                                              <  1:348228/141‑1 (MQ=255)                                                                 tgtgcTTTTGTCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTTTTGTATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGa                                                                            <  1:204110/137‑1 (MQ=255)                                                                  tcatttttGTCTTTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTTAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGAt                                                                           <  2:158557/137‑1 (MQ=255)                                                                       tttATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCTTCTTGTGATGTATCACTTAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCttgt                                                                                                      <  2:358549/109‑1 (MQ=12)                                                                       tttATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCttgt                                                                                                      >  1:358549/1‑109 (MQ=255)                                                                       tttATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCttt                                                                      <  1:647950/141‑1 (MQ=255)                                                                         tATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCGTCTTGTGATGTATCACTCAAATTCTTTGCACTTGCTTCTTC‑TTTTGTCGCTGCTTGTTGTGCTTTTAATGCCACTGGTTTTGTttttttct                                                                    >  1:233385/1‑139 (MQ=14)                                                                          ttCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTAtt                                                                   <  1:708994/140‑1 (MQ=255)                                                                            ctttttCTGCTTGTGCTTCTTTTTTAGCTTCTTGAACCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTGTGATTCTTTATTTg                                                                 <  1:411408/138‑1 (MQ=255)                                                                               tttCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCACTGCCACTGCTTTTGATTCTTTATTTGATa                                                              >  1:263472/1‑141 (MQ=255)                                                                                 tCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACa                                                            <  1:450546/141‑1 (MQ=255)                                                                                 tCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTCTATTTGATACa                                                            <  1:633027/141‑1 (MQ=255)                                                                                  ttGCTTGTGCTTCTTTTTTTGCTTCTTGATTCTCTTGTGCCTCTTTTTATGTATCTCTTAAATTATTTGCACTTGCTTCTTC‑TTTTATCTCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTTATACAg                                                           <  2:253775/140‑1 (MQ=11)                                                                                   tGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGc                                                          >  1:391263/1‑141 (MQ=255)                                                                                      ttGTGCTTCTTTTTTAGCTTCTTGAACCTCTTGTGCCTCTTGTGATGTATCACTTAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCcac                                                       >  1:244983/1‑141 (MQ=21)                                                                                       tgtgCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGcttcttc                                                                                                                       >  1:257006/1‑77 (MQ=255)                                                                                       tgtgCTTCTTTTTTAGCATCTTGAATCTCTTGTGCCTCTTGTGATAACTCACTCAAAATATTTGCACTTGCTTCTTC‑TGTTATCGCTGCTTGTTGTGCCTTCATTGCCTCTGCTTTTGATTATTTATTTGATACAGcaccc                                                      >  2:129261/1‑137 (MQ=11)                                                                                              tttttttAGCTTCTTGATCCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTAt                                               <  2:244983/140‑1 (MQ=255)                                                                                               tttttgAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATc                                              <  1:74664/141‑1 (MQ=255)                                                                                                  tttAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTGCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGc                                           >  2:614076/1‑141 (MQ=255)                                                                                                  tttAGCTTCTTGAACCTCTTGTGCCTCTTGTGATGTATCACTTAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGAt                                                               >  2:254875/1‑121 (MQ=2)                                                                                                  tttAGCTTCTTGAACCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGAt                                                               <  1:254875/121‑1 (MQ=255)                                                                                                   ttaatttcttGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCt                                          <  2:305099/136‑1 (MQ=255)                                                                                                   ttAGCTTCTTGACTCTCTTGTGCCTTTTGTGATGTATCACTCTAATTATTTGCACTTGCTTTTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCt                                          <  2:300019/141‑1 (MQ=255)                                                                                                   ttAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCt                                          >  1:291891/1‑141 (MQ=255)                                                                                                     aGCTTCTTGAATCTCTTGTGCCGCTTGGTATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTTTTTCTTTTTTTGATGAAGCTCCCCTTTTTTCTGCttt                                        >  2:426951/1‑140 (MQ=14)                                                                                                           ttGAATCTTTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTTTTCTTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCtt                                   <  2:397588/141‑1 (MQ=255)                                                                                                              aaTCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCCTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGc                               <  1:105344/141‑1 (MQ=255)                                                                                                               aTCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTTTTTTTTTATTTTATACAGCCACACTTTTACCTGCTTTTGCTTGTGCt                              >  2:696072/1‑141 (MQ=14)                                                                                                               aTCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCGTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCt                              >  1:304267/1‑141 (MQ=255)                                                                                                                tctcTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCAGCTTCTGCTTGTGCtt                             >  1:416772/1‑141 (MQ=255)                                                                                                                tctcTTGTGCCTATTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCtt                             >  1:542028/1‑141 (MQ=255)                                                                                                                   ctTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTtctc                          <  1:722176/141‑1 (MQ=255)                                                                                                                     tgtgCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCtt                        <  1:237531/141‑1 (MQ=255)                                                                                                                      ttgCCTCTTGTGATGTATCACTTAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCttt                       <  2:413491/140‑1 (MQ=255)                                                                                                                      gtgCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAg                                                           <  1:542573/105‑1 (MQ=255)                                                                                                                              tgtgATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTTAGcttct               <  1:28670/141‑1 (MQ=255)                                                                                                                              tgtgATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTTAGcttct               <  1:402917/141‑1 (MQ=255)                                                                                                                               gtgATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTTAGcttctt              >  1:649935/1‑141 (MQ=255)                                                                                                                                tgATGTATCACTCAAATTATTTGCGCTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTAGGCACTACTTCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTTAGCTTCTTg             <  1:178234/141‑1 (MQ=18)                                                                                                                                   tGTATCACTCTAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGTTTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTTAGCTTCTTGAAt          <  2:397684/141‑1 (MQ=255)                                                                                                                                        cACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATCCACCAACACTTTTAACTAAAGCTACTTGTGCTACTCTTTTAGCTTCTCGAATCTCtt     <  1:561351/141‑1 (MQ=14)                                                                                                                                        cACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTTAGCTTCTTGAATCTCtt     <  1:403458/141‑1 (MQ=255)                                                                                                                                        cACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGGGCGGCTCTTTTAGCTTCTTGAATCTCtt     <  1:183771/141‑1 (MQ=255)                                                                                                                                        cACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGATTTTGATTCTTTATTTGATACATCCACACTTTTATCCGCTTCTTCTTGTGCTTCTCTTTTATCTTCTTTTATCTAtt     >  1:159790/1‑141 (MQ=17)                                                                                                                                           tCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTTAGCTTCTTGAATCTCTtgtg  <  1:604177/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                             CTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTTCTCTTTTAGCTTCTTGAATCTCTTGTG  >  USA300TCH1516_ALE/1857728‑1858006

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: ‑