Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,012,563	(G)6→5	pseudogene (62/279 nt)	intG →	putative defective phage integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,012,558	0	G	.	100.0%	69.6 / NA	17	pseudogene (57/279 nt)	intG	putative defective phage integrase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (9/8);  total (9/8)

TCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTA  >  NC_000913/2012480‑2012621                                                                               |                                                                tCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAgg                                                                <  2:352854/80‑1 (MQ=255)  ccAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAgggg                                                              >  2:352870/1‑81 (MQ=255)  ccAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAgggg                                                              >  2:352869/1‑81 (MQ=255)            cTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑GGGGGTTATCGCGt                                                   <  2:352855/81‑1 (MQ=255)              gTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑GGGGGTTATCGCGta                                                  >  1:352880/1‑80 (MQ=255)                     cTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATc                                          >  1:352890/1‑81 (MQ=255)                            cGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATCGTGGATg                                   >  2:352889/1‑81 (MQ=255)                               aacaacATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATCGTGGATgg                                  >  2:352878/1‑79 (MQ=255)                                acaacaTCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATCGTGGATGGCAg                               <  1:352856/81‑1 (MQ=255)                                      tCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACg                         <  2:352857/81‑1 (MQ=255)                                           cGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAg                    >  1:352875/1‑81 (MQ=255)                                            gtggtgATGTGTCAAATGAGACGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAgg                   <  2:352858/81‑1 (MQ=255)                                               gtgATGTGTCAAATGAGACGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATc                <  1:352859/81‑1 (MQ=255)                                                  aTGTGTCAAATGAGACGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAgg             >  2:352879/1‑81 (MQ=255)                                                    gtgtCAAATGAGACGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTa           >  2:352888/1‑81 (MQ=255)                                                       tCAAATGAGACGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATcc        <  2:352860/81‑1 (MQ=255)                                                       tCAAATGAGACGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATcc        <  1:352861/81‑1 (MQ=255)                                                             gagaCGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCAtttt   >  1:352927/1‑80 (MQ=255)                                                             gagaCGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCAtttt   >  2:352873/1‑80 (MQ=255)                                                              agaCGCTCTGATGTTCA‑GGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTa  <  1:352862/80‑1 (MQ=255)                                                                               |                                                                TCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTA  >  NC_000913/2012480‑2012621

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑