Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,929,842	Δ1 bp	100%	intergenic (‑925/‑243)	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	1,929,842	0	T	.	51.0%	90.6 / 113.2	51	intergenic (‑925/‑243)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (13/12);  new base . (7/19);  total (20/31)
Fisher's exact test for biased strand distribution p-value = 8.89e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.54e-01
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

GTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCA  >  CP000730/1929728‑1929978                                                                                                                   |                                                                                                                                              gtAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑Gt                                                                                                                  <  1:199667/141‑1 (MQ=255)           cAATCTATCAGCTAGAATCATATAACTCATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAt‑‑t                                                                                                      >  2:245639/1‑141 (MQ=255)             aTCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAt‑‑ttt                                                                                                    >  2:132828/1‑141 (MQ=255)                          aaTCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATa                                                                                       <  2:171573/141‑1 (MQ=255)                                   aCTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGtc                                                                              >  1:39688/1‑141 (MQ=255)                                     ttATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGtcat                                                                            <  1:199923/141‑1 (MQ=255)                                      tATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGtcatc                                                                           <  1:92631/141‑1 (MQ=255)                                        tCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAg                                                                         <  2:208378/141‑1 (MQ=255)                                        tCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAg                                                                         >  1:308208/1‑141 (MQ=255)                                             cggaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCtg                                                                   <  1:181312/129‑1 (MQ=255)                                               gaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg                                                                 <  2:307008/131‑1 (MQ=255)                                                aagtagatatgCTTGTATATTCACAGGTGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGCGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtgt                                                                <  1:232817/132‑2 (MQ=255)                                                aaGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg                                                                 <  2:254744/141‑1 (MQ=255)                                                  gtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctg                                                              >  1:131170/8‑139 (MQ=255)                                                    agatatgCTTGTATCTTCACAGAAGGTATAATAATACAGTCTCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgtt                                                            <  2:14426/136‑5 (MQ=255)                                                     aCTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAtt                                                            >  1:22891/1‑141 (MQ=255)                                                     aCTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAtt                                                            <  2:95373/141‑1 (MQ=255)                                                     aCTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAtt                                                            >  2:222136/1‑141 (MQ=255)                                                      cTGTGCGTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTg                                                           <  2:78453/141‑1 (MQ=255)                                                       tgtgCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCATGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGc                                                          <  2:321466/141‑1 (MQ=255)                                                       tgtgCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGc                                                          <  1:298140/141‑1 (MQ=255)                                                       tatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgttgcg                                                         <  1:315321/139‑8 (MQ=255)                                                        atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCGTAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt                                                        >  1:31670/2‑141 (MQ=255)                                                           cTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatt                                                     >  1:15080/1‑141 (MQ=255)                                                                    tcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg                                                                 <  2:250434/115‑1 (MQ=255)                                                                    tcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg                                                                 >  1:250434/6‑120 (MQ=255)                                                                     cacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTg                                           >  2:173140/5‑141 (MQ=255)                                                                       ccGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTgg                                          >  1:60036/1‑141 (MQ=255)                                                                       cagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc                                         <  2:215288/139‑1 (MQ=255)                                                                        agatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCt                                        <  2:316340/140‑1 (MQ=255)                                                                           tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag                                     <  2:115722/138‑4 (MQ=255)                                                                           tgatATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTaa                                      >  2:99658/1‑141 (MQ=255)                                                                              tataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaa                                  <  1:280839/141‑2 (MQ=255)                                                                                 aataatAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACg                               >  1:93037/1‑141 (MQ=255)                                                                                  ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc                              <  2:36173/137‑1 (MQ=255)                                                                                  ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc                              <  2:301488/137‑1 (MQ=255)                                                                                  ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc                              <  1:158128/137‑1 (MQ=255)                                                                                  ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑C‑TT‑‑TGCTAATCATTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa                             <  2:283603/137‑1 (MQ=255)                                                                                   taatagTGTCGCCTATCTTTAAGGCGTCAATT‑‑GAAGAAGAGAGGAGGTGCATTAC‑T‑ATGCTAATCAT‑‑TTTCGTTCAAATCATAGCCCCAGTCATCAGTGGCTGTGCTATTGCGTATTATACTTATTGGCTTAGTAAACGCa                             <  2:44104/138‑1 (MQ=255)                                                                                      tagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaaca                          <  1:304971/141‑3 (MQ=255)                                                                                      tagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaaca                          <  1:204486/141‑3 (MQ=255)                                                                                        gagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaa                        >  2:263415/1‑137 (MQ=255)                                                                                        gagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaa                        <  1:232403/141‑5 (MQ=255)                                                                                         agTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCGGTGGCTGTGCTGTTGCAAATTATGCTTATTGGCTTCGTAAACGCaacaaat                       <  2:52958/141‑6 (MQ=255)                                                                                          gTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGTCTAAGTAGACGCAATACaa                       >  2:170569/1‑141 (MQ=255)                                                                                          gTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACaa                       >  2:170563/1‑141 (MQ=255)                                                                                            cGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCAATTGCGTTTTTTTCTTATTGGCTAAGTACACGCAATACaaaa                     >  1:302135/1‑141 (MQ=255)                                                                                                 gagagataGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGt                >  2:242800/8‑141 (MQ=255)                                                                                                          gCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAg       >  2:214335/1‑141 (MQ=255)                                                                                                             tCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCg    <  1:305019/141‑1 (MQ=255)                                                                                                               aaTTTAGTCGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCa  <  1:300793/141‑1 (MQ=255)                                                                                                                   |                                                                                                                                              GTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCA  >  CP000730/1929728‑1929978

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: ‑