Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,729,373	+C	intergenic (‑195/+247)	rrsG ← / ← clpB	16S ribosomal RNA/ClpB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,729,371	1	.	C	96.7%	147.8 / ‑0.2	60	intergenic (‑193/+249)	rrsG/clpB	16S ribosomal RNA/ClpB
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base C (29/29);  total (30/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TGCCGCTTCGCTTTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTT‑C‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAACCCCGCCGACCCGGCG  >  NC_000913/2729324‑2729441                                                 |                                                                        tGCCGCTTCGCTTTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGc                                             <  2:3902640/76‑1 (MQ=0)   ccGCTTCGCTTTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCtt                                           <  1:3102864/76‑1 (MQ=255)   ccGCTTCGCTTTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCtt                                           <  2:2695393/76‑1 (MQ=255)    cgcttcgcttTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCttt                                          >  1:286913/1‑76 (MQ=255)     gcttcgcttTTTCTCAGCGGCGCGTGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCtttt                                         >  1:1264199/1‑76 (MQ=11)     gcttcgcttTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCtttt                                         >  1:542567/1‑76 (MQ=255)     gcttcgcttTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCtttt                                         >  2:450563/1‑76 (MQ=255)      cttcgcttTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTtc                                        <  2:2326345/76‑1 (MQ=255)       ttcgcttTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTtct                                       >  1:2997937/1‑76 (MQ=255)       ttcgcttTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTtct                                       <  2:2413475/76‑1 (MQ=255)        tcgcttTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTtctc                                      <  1:1306612/76‑1 (MQ=255)        tcgcttTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTtctc                                      >  1:5250745/1‑76 (MQ=255)         cgcttTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTctct                                     >  2:2471399/1‑76 (MQ=255)         cgcttTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTctct                                     <  1:3506951/76‑1 (MQ=255)          gcttTTTCTCAGCGGCGCGGGGTGTGCATAATACGGCTT‑CACGCTACAGAGTCAGGCATTTCTTTGCTTTTGTCTg                                    <  2:866889/76‑1 (MQ=14)           cttTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGt                                   <  1:1318158/76‑1 (MQ=255)           cttTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGt                                   <  1:433308/76‑1 (MQ=255)            tttttCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGtt                                  <  1:3327060/76‑1 (MQ=255)             ttttCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTg                                 >  1:2525379/1‑76 (MQ=255)              tttCTGAGCGTCTCGGGGTGTGCATAATACGCCTTCC‑CGCTCCAGAGTCAAGCATTTGTTTGCTTTTCTCTGTTga                                <  2:1819035/76‑1 (MQ=14)              tttCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTga                                <  1:4381916/76‑1 (MQ=255)              tttCTCAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTga                                >  1:3399888/1‑76 (MQ=255)              gttCTCAGCGGCGCGGGGAGTGCATAAGACGCCTTCC‑CGCTACAGAGCCAAGAATTTCTTTGCTTCTCTGTGGTga                                >  1:1819035/2‑76 (MQ=2)               ttCTCAGCGGCGCGGGGAGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTgag                               >  2:878771/1‑76 (MQ=17)                  tcAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGAtt                            <  1:3386838/76‑1 (MQ=255)                  tcAGCGGCGCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGAtt                            >  1:5716623/1‑76 (MQ=255)                     gcggcgCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGGTtctc                         >  1:398133/1‑76 (MQ=17)                     gcggcgCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATtctc                         <  1:5520952/76‑1 (MQ=255)                      cggcgCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCa                        >  1:1362153/1‑76 (MQ=255)                      cggcgCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCa                        >  1:1362512/1‑76 (MQ=255)                      cggcgCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCa                        <  2:3795407/76‑1 (MQ=255)                       ggcgCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCCAGCCTTTCTTTGCTTTTCTCTGTTGAGATTATCAg                       >  1:2626346/1‑76 (MQ=18)                       ggcgCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAg                       <  1:3473016/76‑1 (MQ=255)                       ggcgCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAg                       >  2:3473016/1‑76 (MQ=255)                       ggcgCGGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAg                       >  2:2208846/1‑76 (MQ=255)                          gcgGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGgag                    >  1:2390994/1‑76 (MQ=255)                           cgGGGTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGgaga                   <  1:1937278/76‑1 (MQ=255)                           cgGGGTATGCATAATACGCCTT‑CACGCTACAGTGACAAGCATCTCTTTGCATCTCTATGTTGAGATTCTCAGgata                   >  1:2902990/1‑74 (MQ=16)                             gggTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAAc                 >  2:3006215/1‑76 (MQ=255)                             gggTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAAc                 <  1:5122843/76‑1 (MQ=255)                             gggTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAAc                 >  1:65002/1‑76 (MQ=255)                              ggcgtgCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGCTGAGAGTCTCAGGAGAAcc                >  2:3218702/4‑76 (MQ=18)                              ggTGTGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAAcc                <  1:4206649/76‑1 (MQ=255)                               gtgtGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAAccc               <  1:3839673/76‑1 (MQ=255)                               gtgtGCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAAccc               >  1:4874779/1‑76 (MQ=255)                                tgtgCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAAcccc              >  2:3347765/1‑76 (MQ=255)                                tgtgCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAAcccc              <  2:3495735/76‑1 (MQ=255)                                tgtgCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAAcccc              <  1:2685069/76‑1 (MQ=255)                                tgtgCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAAcccc              >  1:2704345/1‑76 (MQ=255)                                tgtgCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAAcccc              >  1:2824899/1‑76 (MQ=255)                                 gtgCATATGACGTCTTCC‑CGCTACAGATTCAAGCATTTCTTTGCTTTACTCGGTTGCGATTCTCAGTAGAGcccct             <  1:3075810/76‑2 (MQ=9)                                   gCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAACCccgcc           <  2:3399888/76‑1 (MQ=255)                                   gCATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAACCccgcc           <  1:5831333/76‑1 (MQ=255)                                    cATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAACCccgccg          <  2:3758561/76‑1 (MQ=255)                                    cATAATACGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAACCccgccg          >  2:5606826/1‑76 (MQ=255)                                      taataCGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAACCCCGCCGAc        <  2:2866805/76‑1 (MQ=255)                                        ataCGCCTGCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTCGAGATTCTCAGGAGAACCCCGCCGAccc      <  2:1767254/76‑1 (MQ=21)                                          aCGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAACCCCGCCGACCcgg    <  1:2429292/76‑1 (MQ=255)                                          aCGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAACCCCGCCGACCcgg    >  2:4648501/1‑76 (MQ=255)                                           cGCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAACCCCGCCGACCcggc   <  2:1121639/76‑1 (MQ=255)                                            gCCTTCC‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAACCCCGCCGACCcggcg  >  2:4352536/1‑76 (MQ=255)                                                 |                                                                        TGCCGCTTCGCTTTTTCTCAGCGGCGCGGGGTGTGCATAATACGCCTT‑C‑CGCTACAGAGTCAAGCATTTCTTTGCTTTTCTCTGTTGAGATTCTCAGGAGAACCCCGCCGACCCGGCG  >  NC_000913/2729324‑2729441

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑