Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,490,047	0	T	A	26.1%	39.7 / 14.6	23	G129G (GGA→GGT)	USA300HOU_RS12815	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (10/7);  new base A (3/3);  total (13/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.84e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TTATGTTCTTCAATAGAATAATCATTATACACTTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCAT  >  USA300TCH1516_ALE/2489922‑2490180                                                                                                                              |                                                                                                                                      ttATGTTCTTCAATAGAATAATCATTATACACTTTATTATTACTACCAAATTTATTTGCTTCATTACTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATaa                                                                                                                        <  2:34949/141‑1 (MQ=255) ttATGTTCTTCAATAGAATAATCATTATACACTTTATTATTACTACCAAATTTATTTGCCTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATaa                                                                                                                        <  1:211091/141‑1 (MQ=255)            aaTAGAATAATCATTATACACTTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGc                                                                                                             >  2:32225/1‑141 (MQ=255)               aGAATAATCATTATACACTTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAAc                                                                                                          >  1:137638/1‑141 (MQ=255)               aGAATAATCATTATACACTTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAAc                                                                                                          >  2:112184/1‑141 (MQ=255)                                 tttATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTACATTAAACGGATATATTTGACGTGCAACCGGTGCGGCATTTTGTcc                                                                                        >  2:125641/1‑141 (MQ=255)                                             acCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGc                                                                            >  1:132700/1‑141 (MQ=255)                                                            ttCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGAttt                                                             >  2:131536/1‑141 (MQ=255)                                                                ttattaGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGa                                                         <  2:35715/141‑1 (MQ=255)                                                                   ttaGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCAGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGatta                                                      <  1:57319/141‑1 (MQ=255)                                                                     agctgCATTTAAAGCTGTTTGGAAATTAGGCAATTGTTGTAATGCTTGTGATTTATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGattgtt                                                    >  1:31733/5‑138 (MQ=255)                                                                     agctgCATTTAAAGCTGTTTGGAAATTAGGCAATTGTTGTAATGCTTGTGATTTATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGattgtt                                                    >  1:175868/5‑138 (MQ=255)                                                                     agctgCATTTAAAGCTGTTTGGAAATTAGGCAATTGTTGTAATGCTTGTGATTTATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGattgtt                                                    >  1:145413/5‑138 (MQ=255)                                                                              tAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTg                                           <  1:19250/141‑1 (MQ=255)                                                                                  gCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGtta                                       >  2:157253/1‑141 (MQ=255)                                                                                  gCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGtta                                       >  2:170529/1‑141 (MQ=255)                                                                                     gTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTTCAACGTAACTTGATTTTTGATTATTATTCGCTTGGttatta                                    >  1:97345/1‑141 (MQ=255)                                                                                                       tGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTAttt                  >  2:199980/1‑141 (MQ=255)                                                                                                         cTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTAtttgt                <  2:128256/141‑1 (MQ=255)                                                                                                            tAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTAtttgtttg             <  1:108529/141‑1 (MQ=255)                                                                                                                       atttATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTGTTATTCGCTTGATTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCAt  <  2:145413/140‑1 (MQ=255)                                                                                                                       atttATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTGTTATTCGCTTGATTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCAt  <  2:175868/140‑1 (MQ=255)                                                                                                                       atttATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTGTTATTCGCTTGATTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCAt  <  2:31733/140‑1 (MQ=255)                                                                                                                              |                                                                                                                                      TTATGTTCTTCAATAGAATAATCATTATACACTTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCAT  >  USA300TCH1516_ALE/2489922‑2490180

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑