Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,423,705	+C	noncoding (83/120 nt)	rrfD ←	5S ribosomal RNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,423,701	1	.	C	88.9%	117.7 / 9.6	45	noncoding (87/120 nt)	rrfD	5S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base . (3/2);  new base C (27/13);  total (30/15)
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

TAACCTAAAAAGTGGTGCTGATACCCAGAGTCGAACTGGGGACCTCACCCTTACCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GA‑C‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCAAATTCTGTTT  >  NC_000913/3423568‑3423797                                                                                                                                        |                                                                                                    tAACCTAAAAAGTGGTGCTGATACCCAGAGTCGAACTGGGGACCTCACCCTTACCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GA‑c‑c‑ccca                                                                                             <  2:60664/140‑3 (MQ=255)  aaCCTAAAAAGTGGTGCTGATACCCAGAGTCGAACTGGGGACCTCACCCTTACCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GA‑c‑c‑cccac                                                                                            <  2:917999/140‑4 (MQ=255)   aCCTAAAAAGTGGTGCTGATGCCCAGAGACGTACTGGTAAGCTCACCCTTAACAAGGCTACACTCTCCCACCTGCGCCATAGCAGTTTGCTATATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GA‑c‑c‑cccaca                                                                                           <  2:933779/140‑5 (MQ=16)               gtgCTGATACCCAGAGTCGAACTGGGGACCTCACCCTTACCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGgcg                                                                               <  1:210241/140‑1 (MQ=255)                   tGATACCCAGAGTCGAACTGGGGACCTCACCCTTACCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GA‑CAC‑CC‑ACAGTACCATCGGCGCTAc                                                                           >  1:467725/1‑140 (MQ=255)                     aTACCCAGAGTCGAACTTGGGATCTCACCCTAACCTAGGTTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTTCTCTCGCATGGGGAGGC‑C‑C‑CC‑ACACTACCATCGGCGCTACgg                                                                         <  2:547388/140‑1 (MQ=25)                     aTACCCAGAGTCGAACTGGGGACCTCACCCTTACCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACgg                                                                         >  2:971024/1‑140 (MQ=255)                       aCCCAGAGTCGAACTAGGGACCTCAACCTCACCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCg                                                                       <  1:483864/140‑1 (MQ=25)                          cAGAGTCGAACTGGGGACCTCACCCTTACCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCAACTCTCGCATGGAGAGGC‑C‑C‑CC‑ACAATACCATCGGCGCTACGGCGttt                                                                    >  2:646227/1‑140 (MQ=37)                             agTCGAACTGGGGACCTCACCCTTACCAAGGGTGCGCTCTACCAACCGAGACATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACACTCGCATGTGGA‑GA‑C‑CTCC‑ACACTACCATCTGCGCTACGGCGTTTCAc                                                                 >  2:608218/1‑140 (MQ=25)                               tCGAACTGGGGACCTCACCCTTACCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACtt                                                               >  2:1392849/1‑140 (MQ=255)                               tCGAACTGGGGACCTCACCCTTACCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACtt                                                               >  1:1373242/1‑140 (MQ=255)                               tCGAACTGGGGACCTCACCCTTACCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCCCGCATGGGGA‑GA‑C‑C‑CCAACACTACCATCGGAGCTACGGCGTTTCACtt                                                               >  2:483864/1‑140 (MQ=255)                               tCGAACTGGGGACCTCACCCTTACCAAGGGGGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACtt                                                               >  1:261085/1‑140 (MQ=255)                                         gACCTCACCCTTACCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGT‑GACC‑C‑CC‑AAACTCCCATCGGCGCTAGGGCGGTTCACTTCTGAGTTCgg                                                     >  2:511548/1‑140 (MQ=25)                                            cTCACCCTTACCAAGGGTGCGCTCTGCCAGCTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCAt                                                  <  1:511548/140‑1 (MQ=255)                                             gcACCCTTACCAAGGATGCGCTGTAGCAATTGAGCCAGATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATg                                                 <  1:646227/139‑1 (MQ=18)                                              agcccTTACCAAGGGTGTGCTCCACCAACTGTGCCCTATCAGCACGCTCAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATgg                                                <  2:465351/138‑1 (MQ=17)                                                 ccTTACCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGt                                             <  2:1373242/140‑1 (MQ=255)                                                     aCCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGt                                             <  1:213020/136‑1 (MQ=255)                                                     aCCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGt                                             >  2:213020/1‑136 (MQ=255)                                                      ccAAGGGTGCGCTCTTCCAACTGAGCCATGTCAGCACCCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGt                                        <  1:621323/140‑1 (MQ=18)                                                      ccAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGt                                        >  2:978530/1‑140 (MQ=255)                                                           ggTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGTGTTTCACCTCTGAGGTCGGCAAGGGGTCAGGTgggct                                   >  1:465351/1‑138 (MQ=18)                                                           ggTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGac                                   >  1:273709/1‑140 (MQ=255)                                                               cgcTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGaccacc                               >  2:1381666/1‑140 (MQ=255)                                                               cgcTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGATTCCCTTATGAGTTCGTCATGGGGTCAGGTGGGaccacc                               >  2:595279/1‑140 (MQ=18)                                                               cgcTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCACTACGGCGTTTCACTTATGAGTTCGACATGGGGTCAGGTGGGaccacc                               >  2:566199/1‑140 (MQ=18)                                                                    tACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCt                          >  1:977185/1‑140 (MQ=255)                                                                       cAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACg                       <  1:1328032/140‑1 (MQ=255)                                                                       cAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGATGGGACCACCGCGCTACg                       <  1:1392849/140‑1 (MQ=255)                                                                            gAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACGCTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGgccgc                  >  2:30957/1‑140 (MQ=255)                                                                              gCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCa                >  1:1317724/1‑140 (MQ=255)                                                                              gCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCa                >  1:57997/1‑140 (MQ=255)                                                                              gCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCa                >  2:143043/1‑140 (MQ=255)                                                                              gCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGACATGGGGGCAGTTGGGACCACCGCGCTACGGCCGCCa                >  1:626870/1‑140 (MQ=14)                                                                              accATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGACAGGTGGGACCACTGCGCTACGGCCGCCa                >  1:700509/2‑140 (MQ=255)                                                                                cATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGTGCTACGGCCGCCAgg              >  1:513461/1‑140 (MQ=255)                                                                                   atCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCaa           >  2:780884/1‑140 (MQ=255)                                                                                     cAGCACGCTAAATTTTATGCCTCGCAGTTGCCTACTCCCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCAAAt         <  1:566199/140‑1 (MQ=11)                                                                                     cAGCACGCTAAATTTGATGCCTTGCCGTTACCTACTCGCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCAAAt         <  1:595279/140‑1 (MQ=11)                                                                                       gctcGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCAAATTc       >  1:1080078/4‑140 (MQ=16)                                                                                       gCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCAAATTc       >  1:1071693/1‑140 (MQ=25)                                                                                         aCGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCCTGGGGA‑AACC‑C‑CC‑CCACCACCATCGGCGCTACGCCGTTTCACTTTTGGGCTGGGAATGGGGTCAGGCGGGACCACCCCGCTACGGCCCCCAGGCAATTTCTg     >  2:1006407/1‑140 (MQ=11)                                                                                         aCGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCAAATTCTg     >  2:1264972/1‑140 (MQ=18)                                                                                         aCGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCAAATTCTg     >  1:1178394/1‑140 (MQ=21)                                                                                         aCGCTAAATTTGATGCCTGGCACTTCCCTACCCTCCCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCAAATTCTg     <  2:626870/140‑1 (MQ=11)                                                                                         aCGCTAAATTTGATGCCTGGCAATTCCCTACTCTCTCATTGGGAGGC‑C‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCAAATTCTg     <  2:700509/140‑1 (MQ=11)                                                                                         aCGCTAAATTTGATGCCCGGCACTTCCCTACACTCCCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCAAATTCTg     <  2:402962/140‑1 (MQ=11)                                                                                           gCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCAAATTCTGtt   >  2:1107951/1‑140 (MQ=18)                                                                                            cTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GACC‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCAAATTCTGttt  >  2:893675/1‑140 (MQ=17)                                                                                                                                        |                                                                                                    TAACCTAAAAAGTGGTGCTGATACCCAGAGTCGAACTGGGGACCTCACCCTTACCAAGGGTGCGCTCTACCAACTGAGCCATATCAGCACGCTAAATTTGATGCCTGGCAGTTCCCTACTCTCGCATGGGGA‑GA‑C‑C‑CC‑ACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCAAATTCTGTTT  >  NC_000913/3423568‑3423797

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑