Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,579,073	T→C	12.7%	D85G (GAT→GGT)	USA300HOU_1445 ←	major tail protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,579,073	0	T	C	12.7%	67.3 / 4.7	32	D85G (GAT→GGT)	USA300HOU_1445	major tail protein
Reads supporting (aligned to +/- strand):  ref base T (11/16);  new base C (2/2);  total (13/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.85e-01

AAGGCTACATATACCGGCTGACCTGTTAAACCATCTTCCGATTCGCCAATTACTGTTACATACGGTGCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATACACGTTTGTTAGATGCAAACATATCTACTAAATCTGGTGCTAAACCTGTGATATTTAGGTCAACTGTAC  >  CP000730/1578938‑1579211                                                                                                                                        |                                                                                                                                           aagGCTACATATACCGGCTGACCTGTTAAACCATCTTCCGATTCGCCAATTACTGTTACATACGGTGCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAAtcatca                                                                                                                                       <  1:328289/141‑1 (MQ=255)   ggCTACATATACCGGCTGACCTGTTAAACCATCTTCCGATTCGCCAATTACTGTTACATACGGTGCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACt                                                                                                                                     <  2:195680/141‑1 (MQ=255)       aCATATACCGGCTGACCTGTTAAACCATCTTCCGATTCGCCAATTACTGTTACATACGGTGCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGa                                                                                                                                 <  1:125546/141‑1 (MQ=255)              ccGGCTGACCTGTTAAACCATCTTCCGATTCGCCAATTACTGTTACATACGGTGCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTGGGAATATTGa                                                                                                                          <  2:269801/141‑1 (MQ=255)                 gCTGCCCTGTTAAACCATCTTCCGATTCGCCAATTACTGTTACATAAGGTGCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTCCGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGaaaa                                                                                                                       <  2:164512/141‑1 (MQ=255)                  cTGACCTGTTCAACCATCTTCCGATTCGCCAATTACTGTTACATACGGTGCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAAt                                                                                                                      <  2:95213/141‑1 (MQ=255)                                  tCTTCCGATTCGCCAATTACTGTTACATACGGTGCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTa                                                                                                      <  1:145315/141‑1 (MQ=255)                                  tCTTCCGATTCGCCAATTACTGTTACATACGGTGCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTa                                                                                                      >  2:195420/1‑141 (MQ=255)                                              ccAATTACTGTTACATACGGTGCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTa                                                                                          <  1:261778/141‑1 (MQ=255)                                                  ttACTGTTACATACGGTGCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTATTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCtt                                                                                      >  2:309748/1‑141 (MQ=255)                                                    aCTGTTACATACGGTGCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGt                                                                                    <  2:144981/141‑1 (MQ=255)                                                         tACATACGGTGCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTATTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGtttttt                                                                               <  1:101048/141‑1 (MQ=255)                                                                   gCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACATTGTTTTTTCATCCATaca                                                                     >  2:281629/1‑141 (MQ=255)                                                                          tATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAACCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGtt                                                                                   <  1:122033/120‑1 (MQ=255)                                                                          tATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAACCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGtt                                                                                   >  2:122033/1‑120 (MQ=255)                                                                          tATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAACCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGtt                                                                                   >  2:122155/1‑120 (MQ=255)                                                                          tATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAACCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGtt                                                                                   <  1:122155/120‑1 (MQ=255)                                                                            ttCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAAACACTGTGTTTACAGCTCCACTTGATATATTTAAAAGACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATACACGTTTGTTa                                                            <  1:64043/141‑1 (MQ=255)                                                                            ttCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGCACGTCCAATAACTGTGTTTAATTCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATACACGTTTGTTa                                                            <  1:64044/141‑1 (MQ=255)                                                                              ctctcCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATACACGTTTGTTAGa                                                          >  1:246173/1‑141 (MQ=255)                                                                                   cTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGCATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATACACGTTTGTTAGATGCaa                                                     >  1:36824/1‑141 (MQ=255)                                                                                     aCCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATACACGTTTGTTAGATGCAAAc                                                   >  1:285272/1‑141 (MQ=255)                                                                                       ccAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATACACGTTTGTTAGATGCAAACat                                                 >  1:220449/1‑141 (MQ=255)                                                                                          tgctGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATCCACGTTTGTTAGATGCAAACATATc                                              <  2:61364/138‑1 (MQ=255)                                                                                          aGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTAACTTGTTTTTTCATCCATACACGTTTGTTAGATGCAAACATATc                                              <  2:61365/141‑1 (MQ=255)                                                                                             tGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATACACGTTTGTTAGATGCAAACATATctac                                           <  2:159972/141‑1 (MQ=255)                                                                                               tACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATACACGTTTGTTAGATGCAAACATATctacta                                         <  1:49502/141‑1 (MQ=255)                                                                                                aCCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAACTACTCATGTCAGACTTAACTTCATTCGTACCTTGTTTTTTCATCCATACACGTTTGTTAGATGCAAACATATCTACTaa                                        >  1:21213/1‑141 (MQ=255)                                                                                                aCCATTTTTATCTATAGTACGTCCAATAACTGTGTTCAAATCATCTCTTGTACTAATGAAAATACTCATGTCAAACTTAATTTCATTAGCACCTTGCTTGATCATCCAAACACGGTTGCTAGATACAAACATATcttccat                                        >  2:3545/1‑136 (MQ=255)                                                                                                  cATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATACACGTTTGTTAGATGCAAACATATCTACTAAAt                                      >  2:159490/1‑141 (MQ=255)                                                                                                   aTTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATACACGTTTGTTAGATGCAAACATATCTACTAAATc                                     <  2:303417/141‑1 (MQ=255)                                                                                                                      ccAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATACACGTTTGTTAGATGCAAACATATCTACTAAATCTGGTGCTAAACCTGTGata                  >  1:320891/1‑141 (MQ=255)                                                                                                                                      aaTCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATACACGTTTGTTAGATGCAAACATATCTACTAAATCTGGTGCTAAACCTGTGATATTTAGGTCAACTGTac  <  2:273813/141‑1 (MQ=255)                                                                                                                                        |                                                                                                                                           AAGGCTACATATACCGGCTGACCTGTTAAACCATCTTCCGATTCGCCAATTACTGTTACATACGGTGCTCTTGTATTCTCTCCTACCCAAGATGTACCATTTTTATCTTTAGTACGTCCAATAACTGTGTTTAAATCATCACTTGGAATATTGAAAATACTCATGTCAGACTTAACTTCATTAGTACCTTGTTTTTTCATCCATACACGTTTGTTAGATGCAAACATATCTACTAAATCTGGTGCTAAACCTGTGATATTTAGGTCAACTGTAC  >  CP000730/1578938‑1579211

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: ‑