Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	654,252	C→T	58.0%	S362L (TCG→TTG)	USA300HOU_0591 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	654,252	0	C	T	58.0%	15.1 / 39.6	38	S362L (TCG→TTG)	USA300HOU_0591	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (8/8);  new base T (10/12);  total (18/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

TAATGTGTTTATAGAAAATGGTAGTAAATTTGCAAAAGGCGGAAAATACCTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTGGCTATGAGTACAGTATTTG  >  CP000730/654115‑654383                                                                                                                                          |                                                                                                                                    taaatggtTTATAGAAAATGGTAGTAAATTTGCAAAAGGCGGAAAATACCTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGTTCTGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCa                                                                                                                                  <  1:96460/135‑1 (MQ=255)              gAAAATGGTAGTAAATTTGCAAAAGGCGGAAAATACCTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACg                                                                                                                     <  1:137113/141‑1 (MQ=255)                    ggTAGTAAATTTGCAAAAGGCGGAAAATACCTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGAGGCTTGCa                                                                                                               >  2:219463/1‑141 (MQ=255)                        gtaAATTTGCAAAAGGCGGAAAATACCTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTg                                                                                                           <  1:47427/141‑1 (MQ=255)                                    aaGGCAGAAAATACCTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGa                                                                                               <  2:263749/141‑1 (MQ=255)                                           aaaaTACCTAGGTAAAGGTGTTGCTGGTGTAGGATATGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGAgagcagc                                                                                        >  2:211036/1‑140 (MQ=255)                                                 ccTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGc                                                                                  <  1:192100/141‑1 (MQ=255)                                                  cTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTTGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGCCAGCAGTTGGGGCt                                                                                 >  1:265479/1‑141 (MQ=255)                                                  cTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCGGCTGGATCTGCAGGGACAGCCGTTGGAGCt                                                                                 >  2:174955/1‑141 (MQ=255)                                                  cTAGGTAAAGGTGTGGCTGGAGTAGGAGATGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGCGGCGATGTTGCATAATAGTATAACGCTTGCAGCTGGATCTGAGGGGGCACCAGTAGGAGCt                                                                                 >  2:234149/1‑141 (MQ=255)                                                    aGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTgg                                                                               <  1:106730/141‑1 (MQ=255)                                                      gTAAAGGTGTTGGTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGGTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGAt                                                                             <  2:92386/141‑1 (MQ=255)                                                          aGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAgg                                                                         >  1:150064/1‑140 (MQ=255)                                                             ggtTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGAc                                                                      <  1:230370/140‑1 (MQ=255)                                                              gtTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACt                                                                     <  1:17647/141‑1 (MQ=255)                                                              gtTGCTGGTGTAGGATTTGGTATAGGTATGGATGCTGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACt                                                                     <  2:76339/141‑1 (MQ=255)                                                               ttGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGGCtt                                                                    >  1:121897/1‑141 (MQ=255)                                                               ttGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGCTCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACtt                                                                    <  1:265336/141‑1 (MQ=255)                                                                  cTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTg                                                                 >  1:241354/1‑141 (MQ=255)                                                                        tAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAg                                                           >  2:262375/1‑141 (MQ=255)                                                                              ttGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACCTTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGAGCTGCAGGGGAAGCAGTTGGAGCTGGATTAGCGTCTTTTGTTTTAGgtagta                                                     >  1:119062/1‑141 (MQ=255)                                                                                   ataGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGTGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATGAGCGACTTTTGTTTTAGGAAGTAATCCa                                                >  1:158489/1‑141 (MQ=255)                                                                                      ggTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGGGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTa                                             >  1:73475/1‑141 (MQ=255)                                                                                           gtatgATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATg                                        >  1:157754/1‑141 (MQ=255)                                                                                           gtatgATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCAACTTTTGTTTTAGGAAGTAATCCAGTAGGATg                                        >  1:19454/1‑141 (MQ=255)                                                                                             atgatgACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATggg                                      >  2:19685/1‑141 (MQ=255)                                                                                                atgaCCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGa                                   >  2:2104/1‑141 (MQ=255)                                                                                                            atgatgATAAAACATTTGGGGGGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGtt                       <  1:236173/141‑1 (MQ=255)                                                                                                               atgatAAACCATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTgg                    <  1:219613/141‑1 (MQ=255)                                                                                                               atgatAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTgg                    <  2:81209/141‑1 (MQ=255)                                                                                                               atgatAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTgg                    <  2:196903/141‑1 (MQ=255)                                                                                                                tgatAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTGGc                   <  1:262375/141‑1 (MQ=255)                                                                                                                 gatAAAACATTTGGAGAGGCGTTGTCTCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTGGCt                  <  1:265561/141‑1 (MQ=255)                                                                                                                       aCATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCCGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTGGCTATGAGt            >  2:35396/1‑141 (MQ=255)                                                                                                                           ttGGAGAGGCGTTGTTGCAGAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTGGCTATGAGTACAg        <  1:229296/141‑1 (MQ=255)                                                                                                                           ttGGAGAGGCGTTGTTGCACAATGGTATGACTCCTGCAGCTTGGTCGTCACGGACAACAGTTGGAGCTGGATTACCGACTTTTGTTTTAGGAAGTAATCCACTAGGATCGGTGATTTTAGCAGGTTTGGCTATGAGTACAg        <  2:6823/141‑1 (MQ=255)                                                                                                                           ttGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTGGCTATGAGTACAg        >  1:22329/1‑141 (MQ=255)                                                                                                                                 agGCGTTTTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCCGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAAACCAGCAGGATGGGTGATTTTAGCAGGTTTGGCTATGAGTACACTAtttt  <  2:18455/141‑2 (MQ=255)                                                                                                                                          |                                                                                                                                    TAATGTGTTTATAGAAAATGGTAGTAAATTTGCAAAAGGCGGAAAATACCTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTGGCTATGAGTACAGTATTTG  >  CP000730/654115‑654383

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: ‑