Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,009,940	G→A	14.2%	R73H (CGT→CAT)	rluA1 →	pseudouridylate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,009,940	0	G	A	14.2%	72.9 / 3.1	28	R73H (CGT→CAT)	rluA1	pseudouridylate synthase
Reads supporting (aligned to +/- strand):  ref base G (13/11);  new base A (2/2);  total (15/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.98e-01

AAAAATAATGGCGCTTTAATTGTTAATGATGAACCAGTCACAGTGCGTAAGCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCAAAATTGTACGCCTTCGAGAGAACATCCTCATGAAAGTTTAATCGAACAAGT  >  CP000730/1009813‑1010051                                                                                                                                |                                                                                                                atttttaatGGCGCTTTAATTGTTAATGATGAACCAGTCACAGTGCGTAAGCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTa                                                                                                    >  1:116396/6‑141 (MQ=255)   aaaTAATGGCGCTTTAATTGTTAATGATGAACCAGTCACCGTGCGTAAGCAATTAATGACAAGTGATATATTAGAAATTCATCTACGGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTAtt                                                                                                  >  1:52023/1‑141 (MQ=255)   aaaTAATGGCGCTTTAATTGTTAATGATGAACCAGTCACAGTGCGTAAGCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTAtt                                                                                                  >  1:200914/1‑141 (MQ=255)         tGGCGCTTTAATTGTTAATGATGAACCAGTCACAGTGCGTAAGCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGa                                                                                            <  1:94018/141‑1 (MQ=255)         tGGCGCTTTAATTGTTAATGATGAACCAGTCACAGTGCGTAAGCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCATAAGCTAGAAGTATTGTATGa                                                                                            >  1:35926/1‑141 (MQ=255)         tGGCGCTTTAATTGTTAATGATGAACCAGTCACAGTGCGTAAGCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCATAAGCTAGAAGTATTGTATGa                                                                                            >  1:78644/1‑141 (MQ=255)         tGGCGCTTTAATTGTTAATGATGAACCAGTCACAGTGCGTAAGCAATTAATGACAAATGATATATTAGAAAGTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATGCCTTATGCTCGTAAGCTAGAAGTATTGTATGa                                                                                            <  2:63350/141‑1 (MQ=255)          ggCGCTTTAATTGTTAATGATGAACCAGTCACAGTGCGTAAGCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGaa                                                                                           >  2:122083/1‑141 (MQ=255)                        tAATGATGAACCAGTCACAGTGCGTAAGCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTatcat                                                                             >  2:212229/1‑141 (MQ=255)                          atgatgAACCAGTCACAGTGCGTAAGCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTAtcatca                                                                           <  1:56795/141‑1 (MQ=255)                                 aCCAGTCACAGTGCGTAAGCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTAc                                                                    <  2:209155/141‑1 (MQ=255)                                          aGTGCGTAAGCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCaaa                                                           >  1:232139/1‑141 (MQ=255)                                          aGTGCGTAAGCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCaaa                                                           >  1:76227/1‑141 (MQ=255)                                          aGTGCGTAAGCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCaaa                                                           >  1:32181/1‑141 (MQ=255)                                                   gCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCaaaa                                                  >  2:246623/1‑141 (MQ=255)                                                   gCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCaaaa                                                  >  1:187448/1‑141 (MQ=255)                                                   gCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCaaaa                                                  >  1:237007/1‑141 (MQ=255)                                                   gCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCaaaa                                                  >  2:142365/1‑141 (MQ=255)                                                        tAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCAAAATTGTa                                             <  1:78976/141‑1 (MQ=255)                                                        tAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCAAAATTGTa                                             <  1:133604/141‑1 (MQ=255)                                                              cAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCAAAATTGTACGCCtt                                       <  1:143517/141‑1 (MQ=255)                                                              cAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCAAAATTGTACGCCtt                                       <  1:255182/141‑1 (MQ=255)                                                                              aaTTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCAAAATTGTACGCCTTCGAGAGAACATCCTCa                       <  2:172931/141‑1 (MQ=255)                                                                              aaTTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCAAAATTGTACGCCTTCGAGAGAACATCCTCa                       <  2:13514/141‑1 (MQ=255)                                                                                    tttACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCAAAATTGTACGCCTTCGAGAGAACATCCTCATGAAAg                 >  2:151364/1‑141 (MQ=255)                                                                                            gagaAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCAAAATTGTACGCCTTCGAGAGAACATCCTCATGAAAGTTTAATCg         <  2:98993/141‑1 (MQ=255)                                                                                                   aCCGAGTGTTAATTTAATACCTTATGCTCATAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCAAAATTGTACGCCTTCGAGAGAACATCCTCATGAAAGTTTAATCGAACAAGt  <  2:35926/141‑1 (MQ=255)                                                                                                   aCCGAGTGTTAATTTAATACCTTATGCTCATAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCAAAATTGTACGCCTTCGAGAGAACATCCTCATGAAAGTTTAATCGAACAAGt  <  2:78644/141‑1 (MQ=255)                                                                                                                                |                                                                                                                AAAAATAATGGCGCTTTAATTGTTAATGATGAACCAGTCACAGTGCGTAAGCAATTAATGACAAATGATATATTAGAAATTCATTTACCGCGAGAAATACCGAGTGTTAATTTAATACCTTATGCTCGTAAGCTAGAAGTATTGTATGAAGATGCTTTTATCATCATAGTTACTAAACCAAACAATCAAAATTGTACGCCTTCGAGAGAACATCCTCATGAAAGTTTAATCGAACAAGT  >  CP000730/1009813‑1010051

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑