Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	463,014	C→A	66.9%	E47* (GAA→TAA)	USA300HOU_0437 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	463,014	0	C	A	66.9%	18.7 / 14.1	24	E47* (GAA→TAA)	USA300HOU_0437	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (3/5);  new base A (5/11);  total (8/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCTTGTTTAGCTTTGTTGATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTAAAT  >  CP000730/462881‑463147                                                                                                                                      |                                                                                                                                      tCTTGTTTAGCTTTGTTGATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATaagaa                                                                                                                                 >  2:76821/1‑140 (MQ=255)             ttgttgATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGcatcatc                                                                                                                     <  1:136444/140‑1 (MQ=255)              tgttgATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGcatcatca                                                                                                                    >  2:217509/1‑140 (MQ=255)               gttgATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTCTAAGAAGTTTGcatcatcat                                                                                                                   <  1:49196/140‑1 (MQ=255)               gttgATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGcatcatcat                                                                                                                   <  1:248657/140‑1 (MQ=255)                                ttgaATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCAttt                                                                                                  >  2:261415/1‑140 (MQ=255)                                      gtcgtacTTTATCGGCGAATGCTGATTTTCAGTTGTCTTTTGTAGCTTTGTCAGCATTCTTATCTAATAACATATCAATATAACTTAATTCATTTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCTATTTTGAGaa                                                                                            <  2:153839/134‑1 (MQ=255)                                        aGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTCGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATa                                                                                          >  1:186916/1‑140 (MQ=255)                                         gTCCTTTATCGTGGAAGTATGATTTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATaa                                                                                         <  1:150042/140‑1 (MQ=255)                                                          tATGATCTGAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAAGACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTg                                                                        >  2:214253/1‑140 (MQ=255)                                                                             ttcgatcctcgTCTGCATTCTTATCTAATAACACGCTAATATAACTTAATTCATTTTATAAGCAGTTTGCATCATCATGTACTACGAGTCCATTTTGATAATAAACTTTCTCATCTGCTTCATTACCATATCCAACAACg                                                     <  2:189059/130‑1 (MQ=255)                                                                                      ggTCAGTATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCt                                            <  2:270695/140‑1 (MQ=255)                                                                                      ggTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCt                                            <  1:283053/140‑1 (MQ=255)                                                                                        tCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTaa                                          <  1:76821/140‑1 (MQ=255)                                                                                             aTTTTTATCTAATAACACATCAATATAACTTAATTCATGTTCTAAGAAGTTTACATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCGTATGCAACAAGGCCAGTTGCCAAAacac                                     <  1:184637/140‑1 (MQ=255)                                                                                                  tATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTAcc                                <  1:214253/140‑1 (MQ=255)                                                                                                       aataaCACATCATTATCACTTAATTCATGTTCTAAGAAGTTTGCTTCATCATGTAGTACGAGTCCATTTTGAGAATAAACGGTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCGAAAACACCTACCATTGc                           <  1:129434/140‑1 (MQ=255)                                                                                                        ataaCACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGcc                          <  2:252526/140‑1 (MQ=255)                                                                                                          aaCACATCAATATAACTAAATTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACACCAGTCGCTAAAACACCTCCCATTGCCGt                        >  2:52966/1‑140 (MQ=255)                                                                                                                       aaCTTAATTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTaaaaac           >  1:256364/1‑138 (MQ=255)                                                                                                                        aCTTAATTCATGTTATAAGAAGTTTGCATCATCATGTATTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGAGTACCCTATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCt          <  1:148565/140‑1 (MQ=255)                                                                                                                            aaTTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCttttt      >  2:184461/1‑140 (MQ=255)                                                                                                                             aTTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTa     <  1:256584/140‑1 (MQ=255)                                                                                                                                taTGTTATAAGAAGGTTGCATCATCATGTAGTACGAGTCCCTTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTAAAt  <  2:141551/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                                      TCTTGTTTAGCTTTGTTGATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTAAAT  >  CP000730/462881‑463147

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: ‑