Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,929,941	A→T	48.3%	intergenic (‑1024/‑144)	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	1,929,941	0	A	T	48.3%	‑2.3 / 48.5	42	intergenic (‑1024/‑144)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (9/12);  new base T (10/10);  total (20/22)
Fisher's exact test for biased strand distribution p-value = 7.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATTTTTCTTTTTGTAA  >  CP000730/1929802‑1930081                                                                                                                                                 |                                                                                                                                                    tggtagaataagagagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTGCGTTCACAGCATAGCACCAGTCATCAGGGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAg                                                                                                                                                   <  2:305221/129‑1 (MQ=255)  ggtataATAATAAAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTT‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTGTACTTATTGGCTTAgg                                                                                                                                                  >  2:209550/3‑140 (MQ=255)    tataATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTa                                                                                                                                                 >  1:336584/1‑141 (MQ=255)    tataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaa                                                                                                                                                <  2:173789/141‑2 (MQ=255)    taaaataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCGCATCATAGCACCAGTCATCAGTGGCTGTGCCGTTGCGTTTTTTTCTTCATGGCTAAGTa                                                                                                                                                 >  2:24364/4‑141 (MQ=255)     ataataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaa                                                                                                                                               <  2:56056/141‑3 (MQ=255)        ataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTGT‑C‑C‑TGT‑CAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc                                                                                                                                            <  1:82463/141‑1 (MQ=255)        ataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATCGCGTTTTTTTGTTATTGGCTCCGTAGACg                                                                                                                                             >  1:294474/1‑141 (MQ=255)         tagtagAGTCGCCTATCTCTCCGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGc                                                                                                                                            <  2:282721/141‑1 (MQ=255)         tagtagAGTCGCCTATCTCTCAGGCGTCAATTTAGTCGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTTCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGc                                                                                                                                            <  2:268317/141‑1 (MQ=255)         taatagAGTCGCCTATCTCTCAGGCGTCGATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa                                                                                                                                           <  1:249006/138‑1 (MQ=255)         aaagagagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa                                                                                                                                           <  1:37940/137‑1 (MQ=255)             agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGGGTATTATACTTATTGGCTTAGTAAACGCaacaa                                                                                                                                       >  1:159474/1‑138 (MQ=255)             agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑C‑TTTGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTGTTATACTTATTGGCTTAGTGAACGCaacaa                                                                                                                                       >  1:33425/1‑138 (MQ=255)             agagTCGCCTATCTCTCAGGCGTCAATT‑‑CACGAAGAGAGGAGGTGCA‑TTA‑C‑T‑TTACTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAAGGCaacaa                                                                                                                                       >  1:231223/1‑138 (MQ=255)             agagTCGCCTAGCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaa                                                                                                                                       <  1:63764/141‑4 (MQ=255)              gagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaa                                                                                                                                      >  1:270385/1‑137 (MQ=255)                    ccTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGATGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta                                                                                                                                >  1:172911/1‑131 (MQ=255)                    ccTATCTCTCAGGCGTCAA‑‑TAGACGAAGGGAGGAGGTGCA‑TTA‑CTT‑TGC‑TAATCTTTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta                                                                                                                                >  1:232189/1‑131 (MQ=255)                      tATCTCTCAGGCGGCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaat                                                                                                                              <  1:222125/141‑13 (MQ=255)                      tATCTCTAAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaat                                                                                                                              <  2:94746/141‑13 (MQ=255)                       ttctctcAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATTGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGt                                                                                                                          <  2:313064/140‑1 (MQ=255)                       aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                                                             >  1:221566/1‑128 (MQ=255)                       aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                                                             >  1:32157/1‑128 (MQ=255)                       aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCAGCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                                                             <  1:346969/141‑14 (MQ=255)                          tctcAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTCTTTTCTTATTCGCTAAGTGGACGCACT‑‑CCAC‑‑AATAGGCGAc                                                                                                                       >  2:230209/1‑141 (MQ=255)                                 cGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGTCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGc                                                                                                              >  2:347322/1‑141 (MQ=255)                                     aaTTTAGACGCAGAAAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCCTTCACATCAAAAAAAAAAAAAAAAGTGGCTGGGACAGTGCGTTTTTTTCTTACTGGCTACGTAGAAAAAAT‑‑ACAA‑‑AGCCGGTTTCA‑TAT‑Agaaaaa                                                                                                          <  2:155225/141‑6 (MQ=255)                                                               taA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGc                                                                                <  2:212254/141‑1 (MQ=255)                                                                               tATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAggg                                                                    <  1:249357/141‑1 (MQ=255)                                                                                 ttttCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGa                                                                  <  1:171248/141‑1 (MQ=255)                                                                                 ttttCGTTCACACCCTCGCACCAGTCATCAGTGGCTGTGCCATTGCGTTCTTTTCTTATTGGCTAAGTAGACGCAAT‑‑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)                                                                                                                                          aTTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATTTTTCtt         >  2:121646/1‑141 (MQ=255)                                                                                                                                                 aaGTAGACCAAAT‑‑ACAA‑‑AATAGGTTACA‑AGT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAATTTGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGGCTTAATTATACTGCTAATTTTTCTTTTTGTaa  <  2:351220/141‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                    TGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATTTTTCTTTTTGTAA  >  CP000730/1929802‑1930081

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑