Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,448,805	T→C	12.8%	N153D (AAT→GAT)	USA300HOU_1346 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,448,805	0	T	C	12.8%	84.2 / 6.3	39	N153D (AAT→GAT)	USA300HOU_1346	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (23/11);  new base C (3/2);  total (26/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.43e-01

GTATTTCGCCACCTAGACCACCCGTTCCAACTTTGAATACTTGGACATGATAGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACGCCATAATTATTCTCGTTTGAATATATTGAGAAAATATGACCATTGTT  >  CP000730/1448667‑1448937                                                                                                                                           |                                                                                                                                     gTATTTCGCCACCTAGACCACCCGTTCCAACTTTGAATACTTGGACATGATAGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGCCCTGTAATATCTACATGATTCa                                                                                                                                    >  2:199230/1‑141 (MQ=255) gTATTTCGCCACCTAGACCACCCGTTCCAACTTTGAATACTTGGACATGATAGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTAAAGTCCGAATATATTTGTTAAAATTTGACCTGTATTATCCACATACTTCa                                                                                                                                    >  2:215183/1‑141 (MQ=255)     ttCGCCACCTAGACCACCCGTTCCACCTTTGAATACTTGGACATGATAGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACttt                                                                                                                                <  2:277218/141‑1 (MQ=255)          cACCTAGACCACCCGTTCCAACTTTGAATACTTGGACATGATAGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGaa                                                                                                                           >  1:363586/1‑141 (MQ=255)            ccTAGACCACCCGCTCCAACTTTGAATACTTGGACATGATAATCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATCCACTTTAAGAATc                                                                                                                         <  1:348047/141‑1 (MQ=255)                 accaccCGTTCCAACTTTGAATACTTGGACATGATAGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTgg                                                                                                                    <  1:103143/141‑1 (MQ=255)                      ccGTTCCAACTTTGAATACTTGGACATGATAGTCAGCGTTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATGTCTACATGATTCACTTTAAGAATCACTGGTCCTa                                                                                                               >  2:330662/1‑141 (MQ=255)                      ccGTTCCAACTTTGAATACTTGGACATGATAGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTa                                                                                                               >  1:135417/1‑141 (MQ=255)                           ccAACTTTGATTTCTGGGTCATGATAGTCAGCATTGTCGAATAGTGTGTATTCTACTAATCCTTCAACTCCTAATATCGTTGTTAAAAGTTGCCCTATAATATCTCCAGTACTCACTTTAAGAATCACTGGTCCTAAACCt                                                                                                          <  2:113274/141‑1 (MQ=255)                           ccAACTTTGAATACTTGGACATGATAGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCt                                                                                                          <  2:329064/141‑1 (MQ=255)                              aCTTTGAATACTTGGACATGATAGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGc                                                                                                       >  1:231909/1‑141 (MQ=255)                              aCTTTGAATACTTGGACATGATAGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGc                                                                                                       >  1:31890/1‑141 (MQ=255)                               cTTTGAATACTTGGACCTGATAGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTCCATGATTCAGTTTATGAATCCCTGCTCCTAAACCTTGCa                                                                                                      >  1:28381/1‑141 (MQ=255)                                    aacacgcggACAGGATAGGCAGCATCGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCCACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGa                                                                                                 <  1:182022/134‑1 (MQ=255)                                      tACTTGGACATGATAGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATg                                                                                               >  2:319943/1‑141 (MQ=255)                                        cTTGGACATGATAGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTTACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTa                                                                                             >  1:90156/1‑141 (MQ=255)                                                  acaGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTCAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGAc                                                                                   <  1:179477/139‑1 (MQ=255)                                                    aGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCg                                                                                 >  2:88657/1‑141 (MQ=255)                                                            ttGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATCCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCa                                                                         >  2:163466/1‑141 (MQ=255)                                                              gTCGAAGGGTTGGTATTCTGCAAATACTTCCAGTCCGAATATCTTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACATTGCACTTGATGTAACGGATTGACCGCACTCTCaaa                                                                       >  2:41728/1‑141 (MQ=255)                                                              gTCGAAGGGTTGGTATTCTGCAAATACTTCCAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAAAGGATTGACCGCACTTTCaaa                                                                       >  2:181086/1‑141 (MQ=255)                                                              gTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCaaa                                                                       >  2:89244/1‑141 (MQ=255)                                                                 gAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATCCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAaaga                                                                    >  1:397059/1‑141 (MQ=255)                                                                                  cAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCaa                                                   >  1:155083/1‑141 (MQ=255)                                                                                    aaTACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACg                                                 >  1:102748/1‑141 (MQ=255)                                                                                         ttCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACGCCATa                                            <  1:88657/141‑1 (MQ=255)                                                                                                             ttAAAATTTGACCTGTAATATCTACATGATCCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACGCCATAATTATTCTCGTTTGAatata                        >  2:308976/1‑141 (MQ=255)                                                                                                             ttAAAATTCGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACGCCATAATTATTCTCGTTTGAatata                        <  2:266377/141‑1 (MQ=255)                                                                                                                 aaTTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACGCCATAATTATTCTCGTTTGAATATATTga                    >  1:218358/1‑141 (MQ=255)                                                                                                                  aTTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACGCCATAATTATTCTCGTTTGAATATATTgag                   >  1:254402/1‑141 (MQ=255)                                                                                                                   tttGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACGCCATAATTATTCTCGTTTGAATATATTgaga                  >  2:276970/1‑141 (MQ=255)                                                                                                                    tcgACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACGCCATAATTATTCTCGTTTGAATATATTGAGaa                 <  1:307981/139‑1 (MQ=255)                                                                                                                       aCCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATCCCTAAACCAACGCCATAATTATTCTCGTTTGAATCTATTGGGaaaaa              >  2:188692/1‑140 (MQ=255)                                                                                                                         cTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACGCCATAATTATTCTCGTTTGAATATATTGAGAAAatat            >  1:10236/1‑141 (MQ=255)                                                                                                                               tatCTACATGATTCACTTTAAGAATCACTGGTACTAGAGCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACGCCATAATTATTTTCGTTTGAATATATTGAGAAAATATGTCCAt      >  2:142717/1‑141 (MQ=255)                                                                                                                                atCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACGCCATAATTATTCTCGTTTGAATATATTGAGAAAATATGACCAtt     <  1:267201/141‑1 (MQ=255)                                                                                                                                 tCTACATGATCCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACGCCATAATTATTCTCGTTTGAATATATTGAGAAAATATGACCATTg    <  1:308976/141‑1 (MQ=255)                                                                                                                                  cTACCTGATTCACGTCAAGAATCACTGGTCCTAAACCTTGCACTTGCTGTATCCTTCTGCCGTCGCTCTCAACCAAAGACATCCCTAAACCATCGCCACTCGTTTTCTCGTTGGAATATATTTAGAAAAGATAAccgattt   <  2:155083/141‑6 (MQ=255)                                                                                                                                   tACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACGCCATAATTATTCTCGTTTGAATATATTGAGAAAATATGACCATTGtt  >  1:283347/1‑141 (MQ=255)                                                                                                                                           |                                                                                                                                     GTATTTCGCCACCTAGACCACCCGTTCCAACTTTGAATACTTGGACATGATAGTCAGCATTGTCGAAGGGTTGGTATTCTGCAAATACTTCAAGTCCGAATATATTTGTTAAAATTTGACCTGTAATATCTACATGATTCACTTTAAGAATCACTGGTCCTAAACCTTGCACTTGATGTAACGGATTGACCGCACTCTCAAAAGAAGGCATACCTAAACCAACGCCATAATTATTCTCGTTTGAATATATTGAGAAAATATGACCATTGTT  >  CP000730/1448667‑1448937

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: ‑