Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	129,796	G→C	intergenic (‑209/+212)	spa ← / ← sarS	Immunoglobulin G‑binding protein A/HTH‑type transcriptional regulator SarS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	129,796	0	G	C	97.6%	152.4 / NA	42	intergenic (‑209/+212)	spa/sarS	Immunoglobulin G‑binding protein A/HTH‑type transcriptional regulator SarS
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base C (17/24);  minor base T (0/1);  total (17/25)
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

CTATATTTATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGAGATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAGTTGTT  >  USA300TCH1516_ALE/129657‑129928                                                                                                                                            |                                                                                                                                     cTATATTTATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATAttttt                                                                                                                              >  4:180439/1‑148 (MQ=255) cTATATTTATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATAttttt                                                                                                                              >  3:283332/1‑148 (MQ=255)     atTTATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATAtt                                                                                                                                 <  1:13724/141‑1 (MQ=255)      tttATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATaa                                                                                                                         <  4:268428/148‑1 (MQ=255)          aaaTTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGaa                                                                                                                     <  4:122406/147‑1 (MQ=255)            aTTAAATTTTAAGGTAAGTTTTACAACTTATAAAATAAGTTTTTTGCAGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCACTTAATCTCGCTATTTCGATTAATAAAACCAGATAAAATATAGATATATTTTTtata                                                                                                                          <  2:22799/141‑1 (MQ=255)            aTTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGCAAGATTTAGTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTtata                                                                                                                          <  2:14427/141‑1 (MQ=255)            aTTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAg                                                                                                                   >  4:374935/1‑148 (MQ=255)            aTTAAATTTAAAGGTAAGTTTTACAACTTATAAAAGAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATCTGGACATGTTTTTtata                                                                                                                          <  2:15079/141‑1 (MQ=255)              tAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGACAGCg                                                                                                                 >  4:82490/1‑148 (MQ=255)               aaaTTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCgg                                                                                                                <  3:73014/148‑1 (MQ=255)                     aaaGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATAAAAGCg                                                                                                                 >  2:63022/1‑141 (MQ=255)                      aaGGTAAGTTTTACACCTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGCAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATa                                                                                                         >  4:288158/1‑148 (MQ=255)                      aaGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATa                                                                                                         >  4:327161/1‑148 (MQ=255)                       aGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATAc                                                                                                        <  4:127498/148‑1 (MQ=255)                           aaGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACatat                                                                                                    <  3:88091/148‑1 (MQ=255)                             gTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGa                                                                                                  <  3:395779/148‑1 (MQ=255)                             gTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGa                                                                                                  <  3:169245/148‑1 (MQ=255)                                                          cTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTgg                                                                     <  4:376536/148‑1 (MQ=255)                                                          cTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTgg                                                                     <  3:212773/148‑1 (MQ=255)                                                          cTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTgg                                                                     >  4:273521/1‑148 (MQ=255)                                                          cTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGCTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTgg                                                                     >  3:326715/1‑148 (MQ=255)                                                               aGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCtt                                                                >  4:1406/1‑148 (MQ=255)                                                                     aTTCAGGAAGTAAAAGGCTTCAAAACGCAAAATCACGCTATTTAGATTAATAAAAACAGATAAAAAATAGACATATTTTTTATAATGAGAGCGGTTAAATACATAAGAATCAAACAATATTTTACAAAATAAAGTAGGGCt                                                                 >  2:1516/1‑141 (MQ=255)                                                                          ggAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTg                                                     >  3:334027/1‑148 (MQ=255)                                                                           gAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGa                                                    >  4:298083/1‑148 (MQ=255)                                                                                              cGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATgg                                 <  4:284799/148‑1 (MQ=255)                                                                                               gCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGt                                <  3:180439/148‑1 (MQ=255)                                                                                               gCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGt                                <  4:283332/148‑1 (MQ=255)                                                                                                    aTCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTaa                           <  3:206394/148‑1 (MQ=255)                                                                                                      cACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGt                         <  3:356227/148‑1 (MQ=255)                                                                                                       aCGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTg                        <  3:160112/148‑1 (MQ=255)                                                                                                       aCGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGCGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTg                        <  3:300269/148‑1 (MQ=255)                                                                                                          cTATTTCGATTAATAACAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGata                     >  3:366153/1‑148 (MQ=255)                                                                                                          cTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGata                     >  4:8733/1‑148 (MQ=255)                                                                                                          cTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGata                     >  4:404533/1‑148 (MQ=255)                                                                                                                 gATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTAAGGTTTAATTTCGGAAATGGTTTTAAGTGata                     >  2:22536/1‑141 (MQ=255)                                                                                                                            aCAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAgttgt   <  4:283227/148‑1 (MQ=255)                                                                                                                            aCAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAgttgt   <  4:117326/148‑1 (MQ=255)                                                                                                                             cAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAgttgtt  <  3:298864/148‑1 (MQ=255)                                                                                                                             cAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAgttgtt  <  4:89799/148‑1 (MQ=255)                                                                                                                             cAGATAAAATATAGACATAATTTTTATAATGAAAGCGGTTTAATAAAAAAAAAAAAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAgttgtt  <  4:56664/148‑1 (MQ=255)                                                                                                                                            |                                                                                                                                     CTATATTTATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGAGATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAGTTGTT  >  USA300TCH1516_ALE/129657‑129928

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑