Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,929,930	T→A	58.9%	intergenic (‑1013/‑155)	USA300HOU_1794 ← / → USA300HOU_1796	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,929,930	0	T	A	58.9%	26.7 / 53.0	51	intergenic (‑1013/‑155)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (8/13);  new base A (16/14);  total (24/27)
Fisher's exact test for biased strand distribution p-value = 3.94e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.22e-01

TATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATT  >  CP000730/1929792‑1930068                                                                                                                                                   |                                                                                                                                                  tattcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑C‑T‑T‑‑‑TGCTAATGGTTACTTATCACATCATAGCACCAGTCATCAGGGGCTGGGCTGTTGCGTATTATACtt                                                                                                                                                >  1:99374/9‑141 (MQ=255)     cacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTg                                                                                                                                            >  2:197643/5‑141 (MQ=255)      acagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTTTTGCGTATTATACTTATTgg                                                                                                                                           <  1:217272/138‑1 (MQ=255)       ccGATGATATAATAGTAGAGGCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTAT‑‑TTTCGT‑TCACATCATAGCACCCGTTATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTgg                                                                                                                                           <  2:58816/141‑1 (MQ=255)       cagatggtATAATAATAGAGGCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc                                                                                                                                          <  1:175042/139‑1 (MQ=255)       cagagggtataATAATAGAGTCGCCTATCTCTCCGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc                                                                                                                                          <  2:357515/134‑1 (MQ=255)        cGAGGATATAATAGGAGAGTCGCCGATGTCTCAGGCGGCAATGTAGGCGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTAT‑‑TTTCGT‑TCACATCAGAGCACCAGTCATCAGTGGCTGTGCCACTGCGTTTTTTTCTTATTGGc                                                                                                                                          <  1:270609/141‑1 (MQ=255)        agatggtATAATAAAAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCt                                                                                                                                         >  2:243199/2‑141 (MQ=255)         gatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCtt                                                                                                                                        >  1:87064/1‑140 (MQ=255)          atggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCtta                                                                                                                                       >  1:38217/5‑139 (MQ=255)           tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag                                                                                                                                      >  1:285321/4‑138 (MQ=255)           tggtagaataagagagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTGCGT‑TCACAGCATAGCACCAGTCATCAGGGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAg                                                                                                                                      <  2:305221/129‑1 (MQ=255)           tggcataataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag                                                                                                                                      <  2:241046/137‑4 (MQ=255)            ggtataATAATAAAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTT‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTGTACTTATTGGCTTAgg                                                                                                                                     >  2:209550/3‑140 (MQ=255)              tataATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTa                                                                                                                                    >  1:336584/1‑141 (MQ=255)              tataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaa                                                                                                                                   <  2:173789/141‑2 (MQ=255)              taaaataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTAT‑‑TTTCGT‑TCGCATCATAGCACCAGTCATCAGTGGCTGTGCCGTTGCGTTTTTTTCTTCATGGCTAAGTa                                                                                                                                    >  2:24364/4‑141 (MQ=255)               ataataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaa                                                                                                                                  <  2:56056/141‑3 (MQ=255)                  ataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTGT‑C‑C‑TGT‑CAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc                                                                                                                               <  1:82463/141‑1 (MQ=255)                  ataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCCATCGCGTTTTTTTGTTATTGGCTCCGTAGACg                                                                                                                                >  1:294474/1‑141 (MQ=255)                   tagtagAGTCGCCTATCTCTCCGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGc                                                                                                                               <  2:282721/141‑1 (MQ=255)                   tagtagAGTCGCCTATCTCTCAGGCGTCAATTTAGTCGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTTCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGc                                                                                                                               <  2:268317/141‑1 (MQ=255)                   taatagAGTCGCCTATCTCTCAGGCGTCGATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa                                                                                                                              <  1:249006/138‑1 (MQ=255)                   aaagagagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa                                                                                                                              <  1:37940/137‑1 (MQ=255)                       agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGGGTATTATACTTATTGGCTTAGTAAACGCaacaa                                                                                                                          >  1:159474/1‑138 (MQ=255)                       agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑C‑TTTGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTGTTATACTTATTGGCTTAGTGAACGCaacaa                                                                                                                          >  1:33425/1‑138 (MQ=255)                       agagTCGCCTATCTCTCAGGCGTCAATT‑‑CACGAAGAGAGGAGGTGCA‑TTA‑C‑T‑TTACTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAAGGCaacaa                                                                                                                          >  1:231223/1‑138 (MQ=255)                       agagTCGCCTAGCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaa                                                                                                                          <  1:63764/141‑4 (MQ=255)                        gagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaa                                                                                                                         >  1:270385/1‑137 (MQ=255)                              ccTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGATGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta                                                                                                                   >  1:172911/1‑131 (MQ=255)                              ccTATCTCTCAGGCGTCAA‑‑TAGACGAAGGGAGGAGGTGCA‑TTA‑CTT‑TGC‑TAATCTT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta                                                                                                                   >  1:232189/1‑131 (MQ=255)                                tATCTCTCAGGCGGCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaat                                                                                                                 <  1:222125/141‑13 (MQ=255)                                tATCTCTAAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaat                                                                                                                 <  2:94746/141‑13 (MQ=255)                                 ttctctcAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTAT‑‑TTTCGT‑TCACATCATTGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGt                                                                                                             <  2:313064/140‑1 (MQ=255)                                 aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                                                >  1:221566/1‑128 (MQ=255)                                 aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                                                >  1:32157/1‑128 (MQ=255)                                 aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCAGCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                                                <  1:346969/141‑14 (MQ=255)                                    tctcAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTCTTTTCTTATTCGCTAAGTGGACGCACT‑‑CCAC‑‑AATAGGCGAc                                                                                                          >  2:230209/1‑141 (MQ=255)                                           cGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGTCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGc                                                                                                 >  2:347322/1‑141 (MQ=255)                                               aaTTTAGACGCAGAAAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTAT‑‑TTTCCT‑TCACATCAAAAAAAAAAAAAAAAGTGGCTGGGACAGTGCGTTTTTTTCTTACTGGCTACGTAGAAAAAAT‑‑ACAA‑‑AGCCGGTTTCA‑TAT‑Agaaaaa                                                                                             <  2:155225/141‑6 (MQ=255)                                                                         taA‑G‑G‑TGA‑TGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGc                                                                   <  2:212254/141‑1 (MQ=255)                                                                                         tAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAggg                                                       <  1:249357/141‑1 (MQ=255)                                                                                           t‑‑tttCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGa                                                     <  1:171248/141‑1 (MQ=255)                                                                                           t‑‑tttCGT‑TCACACCCTCGCACCAGTCATCAGTGGCTGTGCCATTGCGTTCTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGa                                                     <  1:24364/141‑1 (MQ=255)                                                                                                           catAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGt                                        >  1:194722/1‑141 (MQ=255)                                                                                                           catAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGGGAGGGGGTTGGTGTATAAGt                                        >  1:91724/1‑141 (MQ=255)                                                                                                            atAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCAACAAATAATTAATAGGCGACTTTATAAGCCAGCAACGA‑AAAAATCCCCACACTACTGC‑AATAGTGAGGGGATGGGTGcat                                            >  2:125072/1‑141 (MQ=255)                                                                                                                cACCAGTCATCAGGGGCTGTGCCATTGCGTTTTTTTCTTAGTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATa                                   <  2:241423/141‑1 (MQ=255)                                                                                                                            gTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGtt                       >  2:309151/1‑141 (MQ=255)                                                                                                                                cTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCt                   <  1:148616/141‑1 (MQ=255)                                                                                                                                       aTTGCGTTTTTTTCTTCTTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATCAGTCATTTCGTAGTTTCGTTGTCTTAATtat            <  2:254164/141‑1 (MQ=255)                                                                                                                                               tttttCTTTTTTGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GAACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATCCTTATTTTCGTTGTCTTAAtttaccttctaa    >  2:16784/1‑131 (MQ=255)                                                                                                                                                 tttCGTATTGGCTAAGGAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAAtt  <  2:336584/141‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                  TATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATT  >  CP000730/1929792‑1930068

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: ‑