Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	566,871	(A)6→5	coding (30/300 nt)	insE‑3 →	DLP12 prophage; IS3 element protein InsE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	566,866	0	A	.	93.3%	43.1 / ‑1.5	15	coding (25/300 nt)	insE‑3	DLP12 prophage; IS3 element protein InsE
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base . (9/5);  minor base T (1/0);  total (10/5)
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

GCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAG  >  NC_000913/566730‑566908                                                                                                                                         |                                           gCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTaaaa                                         <  2:142468/140‑1 (MQ=255)  cTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTaaaaa                                        >  2:684996/1‑140 (MQ=255)   ttCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTaaaaac                                       <  2:639472/140‑2 (MQ=255)           acaGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGT‑AAAAACCCCGTaaa                              <  1:684996/140‑1 (MQ=255)            caGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGT‑AAAAACCCCGTaaaa                             >  1:766638/1‑139 (MQ=255)               gACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAAGCAGT‑AAAAACCCCGTAAACAGc                          >  1:387682/1‑140 (MQ=255)               gACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGT‑AAAAACCCCGTAAACAGc                          >  2:90440/1‑140 (MQ=255)               gACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGT‑AAAAACCCCGTAAACAGc                          >  1:505029/1‑140 (MQ=255)                  gTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACCCACATGACAAAAACAGTATCAACCA‑TTAAAAACCCCGTAAACAGCAtt                       >  2:367519/1‑140 (MQ=255)                    tGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGT‑AAAAACCCCGTAAACAGCa                         >  1:805884/1‑136 (MQ=255)                    tGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGT‑AAAAACCCCGTAAACAGCa                         >  2:555232/1‑136 (MQ=255)                    tGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGT‑AAAAACCCCGTAAACAGCa                         <  1:555232/136‑1 (MQ=255)                    tGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGT‑AAAAACCCCGTAAACAGCa                         <  2:805884/136‑1 (MQ=255)                     gCCGCGGTAACAGGCGCAACCGTAACCTGGTCTTACCAAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGT‑AAAAACCCCGTAAACAGCATTCGc                    <  1:351954/140‑1 (MQ=14)                       cgcgGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGT‑AAAAACCCCGTAAACAGCATTCGCCt                  >  1:835429/1‑140 (MQ=255)                       cgcgGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGT‑AAAAACCCCGTAAACAGCATTCGCCt                  >  2:15175/1‑140 (MQ=255)                                    gcAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGT‑AAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTg     <  2:505029/140‑1 (MQ=21)                                       aCCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGT‑AAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAg  >  2:164427/1‑140 (MQ=17)                                                                                                                                         |                                           GCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAG  >  NC_000913/566730‑566908

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑