Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,941,734	Δ1 bp	noncoding (409/2906 nt)	rrlC →	23S ribosomal RNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,941,734	0	A	.	96.7%	92.4 / ‑3.2	30	noncoding (409/2906 nt)	rrlC	23S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base . (16/13);  total (17/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGAGGGACCATCCTCCAAGGCTAAATA  >  NC_000913/3941663‑3941758                                                                        |                         gTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGAc                     >  1:3082798/1‑76 (MQ=255) gTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGAc                     >  1:5344949/1‑76 (MQ=255) gTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGAc                     <  1:4706735/76‑1 (MQ=255) gTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGAc                     >  1:3604658/1‑76 (MQ=255)  tACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGCATCCTGTCTGAATATGGG‑GGGAcc                    <  1:1132601/76‑1 (MQ=11)   acacAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCa                   >  2:5319468/1‑76 (MQ=255)    cacaAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAt                  >  2:3010828/1‑76 (MQ=255)    cacaAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAt                  <  2:4011404/76‑1 (MQ=9)    cacaAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAt                  <  1:4254036/76‑1 (MQ=255)     acaAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtc                 <  2:130343/76‑1 (MQ=9)     acaAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtc                 <  1:3379268/76‑1 (MQ=255)      caAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcc                >  2:4397010/1‑76 (MQ=255)      caAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcc                >  1:5207622/1‑76 (MQ=255)       aaaaaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcct               >  1:3846884/1‑76 (MQ=255)        gaaaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcctc              >  2:5189822/2‑76 (MQ=255)        aaaaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcctc              >  1:731010/1‑76 (MQ=255)         aaaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcctcc             <  2:4924875/76‑1 (MQ=12)         aaaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcctcc             >  1:1442883/1‑76 (MQ=255)         aaaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcctcc             <  2:1678334/76‑1 (MQ=12)         aaaTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCAtcctcc             >  1:3558045/1‑76 (MQ=255)           aTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCaa           <  2:1733774/76‑1 (MQ=9)           aTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCaa           >  1:4377473/1‑76 (MQ=255)           aTGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCCCCaa           >  2:201327/1‑76 (MQ=11)            tGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCAAg          >  1:3807770/1‑76 (MQ=255)             gCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCAAgg         <  1:2542671/76‑1 (MQ=255)              cacaTATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCAAGGc        <  2:2809045/76‑1 (MQ=9)              cacaTATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCAAGGc        >  1:5384854/1‑76 (MQ=12)               acaTATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCAAGGCt       <  2:1820976/76‑1 (MQ=9)                caTATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGG‑GGGACCATCCTCCAAGGCTa      <  1:3576780/76‑1 (MQ=0)                    ttGTGAGCTCGATGAGTAGGGCGGGCAACGTGGCATCCTGTCCGACTATGCGAGCAACC‑TCCCCCAACGATAAATa  >  2:267044/1‑76 (MQ=2)                                                                        |                         GTACACAAAAATGCACATATTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGAGGGACCATCCTCCAAGGCTAAATA  >  NC_000913/3941663‑3941758

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑