Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,209,679	C→A	noncoding (1533/1542 nt)	rrsE →	16S ribosomal RNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,209,679	0	C	A	97.1%	68.9 / ‑2.7	34	noncoding (1533/1542 nt)	rrsE	16S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (19/14);  total (20/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.00e-01

TTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑CACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCAC  >  NC_000913/4209596‑4209812                                                                                       |                                                                                                                                      ttCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGa                                                                               <  2:238646/140‑1 (MQ=11) ttCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGa                                                                               <  1:726975/140‑1 (MQ=11)   cGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGaaa                                                                             >  1:810782/1‑140 (MQ=17)    gggAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAg                                                                            >  1:38164/1‑140 (MQ=17)         ggCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGaaa                                                                       >  1:674135/1‑140 (MQ=17)                aCCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAgg                                                                >  1:312326/1‑140 (MQ=17)                    cTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTc                                                            <  2:1284379/140‑1 (MQ=18)                              cATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAGGCAAGGCGTCTTGCGAAGCa                                                  <  1:726739/140‑1 (MQ=16)                                tGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGa                                                <  1:248658/140‑1 (MQ=18)                                      gggTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATa                                          >  2:717079/1‑140 (MQ=17)                                      gggTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATa                                          >  2:347648/1‑140 (MQ=17)                                      gggTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATa                                          >  2:178949/1‑140 (MQ=17)                                       ggTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAGAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATAc                                         >  1:1179557/1‑140 (MQ=17)                                                gTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTc                                >  1:1229359/1‑140 (MQ=17)                                                      aGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTag                          <  2:38164/140‑1 (MQ=17)                                                      aGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTag                          <  1:590165/140‑1 (MQ=17)                                                      aGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTag                          <  1:717079/140‑1 (MQ=17)                                                      aGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTag                          <  2:312326/140‑1 (MQ=17)                                                        gTAACCGTAGGGGAACCTGCGGTTGTAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTagag                        <  2:525775/140‑1 (MQ=17)                                                        gTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGCAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTagag                        >  2:1028850/1‑140 (MQ=17)                                                        gTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTagag                        >  2:1188504/1‑140 (MQ=17)                                                        gTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTagag                        <  1:347648/140‑1 (MQ=17)                                                            ccGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGccc                    <  2:409689/140‑1 (MQ=17)                                                              gTAGGGGAACCTGCGGTTGGATAACCTCCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGcc                     >  1:797440/1‑140 (MQ=11)                                                               tAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAgg                 >  2:1373267/1‑140 (MQ=17)                                                                 ggggAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGac               >  2:540790/1‑140 (MQ=17)                                                                     aaCCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCg           <  2:968404/140‑1 (MQ=17)                                                                      aCCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGc          >  1:795881/1‑140 (MQ=17)                                                                      aCCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGc          >  2:479266/1‑140 (MQ=17)                                                                       ccTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGcc         >  1:226873/1‑140 (MQ=17)                                                                       ccTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGcc         >  1:118999/1‑140 (MQ=17)                                                                          gCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCtt      >  1:793672/1‑140 (MQ=17)                                                                              ttGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCAc  <  2:1179557/140‑1 (MQ=17)                                                                              ttGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCAc  >  1:1008191/1‑140 (MQ=17)                                                                                       |                                                                                                                                      TTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑CACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCAC  >  NC_000913/4209596‑4209812

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑