Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,610,079	(T)7→8	coding (447/795 nt)	USA300HOU_2473 ←	lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,610,072	1	.	T	80.8%	67.1 / 13.8	26	coding (454/795 nt)	USA300HOU_2473	lipoprotein
Reads supporting (aligned to +/- strand):  ref base . (0/5);  new base T (9/12);  total (9/17)
Fisher's exact test for biased strand distribution p-value = 1.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.29e-01

ACATTATAATCATCATTATTCAATTGATATTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTC‑TTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATAAAATAATACC  >  CP000730/2609933‑2610206                                                                                                                                             |                                                                                                                                       aCATTATAATCATCATTATTCAATTGATATTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATctc‑t                                                                                                                                       <  1:401261/141‑1 (MQ=255)  cATTATAATCATCATTATTCAATTGATATTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTC‑tt                                                                                                                                      >  1:129186/1‑141 (MQ=255)                 tattCAATTGATATTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCa                                                                                                                        <  1:443134/141‑1 (MQ=255)                  attCAATTGATATTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCAt                                                                                                                       <  1:285014/141‑1 (MQ=255)                       aTTGATATTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGt                                                                                                                  <  2:211122/141‑1 (MQ=255)                           atatTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTC‑TTTTTTTAACTTGTCATTCGGTAGTgg                                                                                                             <  1:162135/141‑1 (MQ=255)                                       aTAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTTTTTTTTTATTTGGTAGTGGCTTCGTTgttt                                                                                                  >  2:253437/1‑138 (MQ=17)                                       aTAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTa                                                                                                  >  1:48742/1‑141 (MQ=255)                                         aaCTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATg                                                                                                <  1:52260/141‑1 (MQ=255)                                               gTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTtta                                                                                          <  1:1073/141‑1 (MQ=255)                                                   aTTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTtattat                                                                                      <  2:178622/141‑1 (MQ=255)                                                     tAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTC‑TTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGtt                                                                                   <  2:392288/141‑1 (MQ=255)                                                                      tCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTTTTTTTTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATa                                                                   >  2:2471/1‑141 (MQ=25)                                                                      tCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATa                                                                   >  1:180296/1‑141 (MQ=255)                                                                            tCTTTATCATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTTGTATGATTTTATTATGTTCCATTTTTGCCGGACACCtttt                                                             <  2:197003/141‑1 (MQ=21)                                                                                  taATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTtcatc                                                       >  1:46094/1‑141 (MQ=255)                                                                                                     aGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTa                                    <  2:381248/141‑1 (MQ=255)                                                                                                      gTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTC‑‑TTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTActg                                 <  2:316643/141‑1 (MQ=255)                                                                                                       ttGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTC‑TTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTActg                                 <  1:410258/141‑1 (MQ=255)                                                                                                               ttGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACGTTTTTTCATCATCCTTTGGTCTGCCGTTActgtcatctg                          <  2:375463/141‑1 (MQ=255)                                                                                                                   aCAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCTTCCTTTGGTCTGCCGTTActgtcatctgtcat                      >  2:138453/1‑141 (MQ=255)                                                                                                                              aaaGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATaa           >  1:144126/1‑141 (MQ=255)                                                                                                                               aaGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATaaa          >  1:228640/1‑141 (MQ=255)                                                                                                                                    ttCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATAAaataat     <  1:83517/141‑1 (MQ=255)                                                                                                                                     tCAATCTCTTTTTTTTAATTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTTTCATTTTTCATTTCACTTTTAAAataata    >  2:309275/1‑141 (MQ=255)                                                                                                                                      cAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATAAAATAATAc   <  2:48742/141‑1 (MQ=255)                                                                                                                                      cAATCTC‑TTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATAAAATAATAcc  <  2:398951/141‑1 (MQ=255)                                                                                                                                       aaTCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATAAAATAATAcc  <  1:230008/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                       ACATTATAATCATCATTATTCAATTGATATTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTC‑TTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATAAAATAATACC  >  CP000730/2609933‑2610206

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑