Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,189,012	G→T	pseudogene (1581/2434 nt)	yqiG →	putative outer membrane usher protein YqiG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,189,012	0	G	T	93.3%	41.6 / NA	15	pseudogene (1581/2434 nt)	yqiG	putative outer membrane usher protein YqiG
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base T (7/7);  total (7/8)
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

AAAAACTTTGTGACAATGAATGAATATATCAATGACACTAACCATTACACGAATTATCAGAATGAAAAAGAGAGTTATATTGTCACGTTTAACCAGTATCTTGAATCATTAAGGTTAAATACATACGTAAGTTTGGCTCGTAATACTTACTGGGACGCCAGCAGTAATGTGAATTATTCATTATCACTTAGCCGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATTTAGCCGAATAAACTGGGAAGAAGACAACCAGGATCAACTGTACCTAAATATTTCGATTCCCTGGGGAACTAGTAGAACATTGAGCTATGGTATGCAACGAAATCAGGATAATGAGATTTCGCATACTGCTTCGTGGTATGACTCTTCCGATCGAAATAATTCCTGGAGCGTTTCTGCTTCAGGCGACAATGATGAATTCAAAGATATGAAAGCGTCACTACGCGCCAGTTATCAGCATAATACCGAG  >  NC_000913/3188765‑3189253                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                  aaaaaCTTTGTGACAATGAATGAATATATCAATGACACTAACCATTACACGAATTATCAGAATGAAAAAGAGAGTTATATTGTCACGTTTAACCAGTATCTTGAATCATTAAGGTTAAATACATACGTAAGTTTGGCTCGTAATTCTTACTGGGACGCCAGCAGTAATGTGAATTATTCATTATCACTTAGCCGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATTTAGCCTAAt                                                                                                                                                                                                                                                <  2:44444/251‑1 (MQ=255)             aCAATGAATGAATATATCAATGACACTAACCATTACACGAATTATCAGAATGAAAAAGAGAGTTATATTGTCACGTTTAACCAGTATCTTGAATCATTAAGGTTAAATACATACGTAAGTTTGGCTCGTAATACTTACTGGGACGCCAGCAGTAATGTGAATTATTCATTATCACTTAGCCGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATTTAGCCTAATAAACTGGgaaga                                                                                                                                                                                                                                    <  1:17175/251‑1 (MQ=255)             aCAATGAATGAATATATCAATGACACTAACCATTACACGAATTATCAGAATGAAAAAGAGAGTTATATTGTCACGTTTAACCAGTATCTTGAATCATTAAGGTTAAATACATACGTAAGTTTGGCTCGTAATACTTACTGGGACGCCAGCAGTAATGTGAATTATTCATTATCACTTAGCCGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATTTAGCCTAATAAACTGGga                                                                                                                                                                                                                                       >  2:208341/1‑248 (MQ=255)                                 tGACACTAACCATTACACGAATTATCAGAATGAAAAAGAGAGTTATATTGTCACGTTTAACCAGTATCTTGAATCATTAAGGTTAAATACATACGTAAGTTTGGCTCGTAATACTTACTGGGACGCCAGCAGTAATGTGAATTATTCATTATCACTTAGCCGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATTTAGCCTAATAAACTGGGAAGAAGACAACCAGGATCAACTGt                                                                                                                                                                                                                >  1:52352/1‑251 (MQ=255)                                                                 aaaaaGAGAGTTATATTGTCACGTTTAACCAGTATCTTGAATCATTAAGGTTAAATACATACGTAAGTTTGGCTCGTAATACTTACTGGGACGCCAGCAGTAATGTGAATTATTCATTATCACTTAGCCGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATTTAGCCTAATAAACTGGGAAGAAGACAACCAGGATCAACTGTACCTAAATATTTCGATTCCCTGGGGAACtagt                                                                                                                                                                                >  1:187016/1‑251 (MQ=255)                                                                                     aCGTTTAACCAGTATCTTGAATCATTAAGGTTAAATACATACGTAAGTTTGGCTCGTAATACTTACTGGGACGCCAGCAGTAATGTGAATTATTCATTATCACTTAGCCGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATTTAGCCTAATAAACTGGGAAGAAGACAACCAGGATCAACTGTACCTAAATATTTCGATTCCCTGGGGAACTAGTAGAACATTGAGCTATGGTAt                                                                                                                                                            >  1:50220/1‑251 (MQ=255)                                                                                      cGTTTAACCAGTATCTTGAATCATTAAGGTTAAATACATACGTAAGTTTGGCTCGTACTACTTACTGGGACGCCAGCAGTAATGTGAATTATTCATTATCACTTAGCCGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATTTAGCCTAATAAACTGGGAAGAAGACAACCAGGATCAACTGTACCTAAATATTTCGATTCCCTGGGGAACTAGTAGAACATTGAGCTATGGTATg                                                                                                                                                           >  2:108125/1‑251 (MQ=255)                                                                                                      tGAATCATTAAGGTTAAATACATACGTAAGTTTGGCTCGTAATACTTACTGGGACGCCAGCAGTAATGTGAATTATTCATTATCACTTAGCCGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATTTAGCCTAATAAACTGGGAAGAAGACAACCAGGATCAACTGTACCTAAATATTTCGATTCCCTGGGGAACTAGTAGAACATTGAGCTATGGTATGCAACGAAATCAgg                                                                                                                                              <  1:216303/248‑1 (MQ=255)                                                                                                               aaGGTTAAATACATACGTAAGTTTGGCTCGTAATCCTTACTGGGACGCCAGCAGTAATGTGAATTATTCATTATCACTTAGCCGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATTTAGCCTAATAAACTGGGAAGAAGACAACCAGGATCAACTGTACCTAAATATTTCGATTCCCTGGGGAACTAGTAGAACATTGAGCTATGGTATGCAACGAAATCAGGATAATGAGAtt                                                                                                                                   <  2:65972/250‑1 (MQ=255)                                                                                                                                      tGGCTCGTAATACTTACTGGGACGCCAGCAGTAATGTGAATTATTCATTATCACTTAGCCGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATTTAGCCTAATAAACTGGGAAGAAGACAACCAGGATCAACTGTACCTAAATATTTCGATTCCCTGGGGAACTAGTAGAACATTGAGCTATGGTATGCAACGAAATCAGGATAATGAGATTTCGCATACTGCTTCGTGGTATGAc                                                                                                           >  2:95405/1‑251 (MQ=255)                                                                                                                                                                               tattCATTATCACTTAGCCGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATTTATCCTAATAAACTGGGAAGAATACAACCAGGATCAACTGTACCTAAATATTTCGATTCCCTGGGGAACTAGTAGAACATTGAGCTATGGTATGCAACGAAATCAGGAGAATGAGATTTCGCATACTGCTTCGTAGTATGACTCTTGCGATCGAAATAACTCCTTGAGCGTTTCtactgcag                                                                   <  2:147092/250‑8 (MQ=255)                                                                                                                                                                                      tATCACTTAGCCGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATTTAGCCTAATAAACTGGGAAGAAGACAACCAGGATCAACTGTACCTAAATATTTCGATTCCCTGGGGAACTAGTAGAACATTGAGCTATGGTATGCAACGAAATCAGGATAATGAGATTTCGCATACTGCTTCGTGGTATGACTCTTCCGATCGAAATAATTCCTGGAGCGTTTCTGCTTCAGGCGACAat                                                           >  1:56259/1‑251 (MQ=255)                                                                                                                                                                                                ccGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATT‑AGCCTAATAAACTGGGAAGAAGACAACCAGGATCAACTGTACCTAAATATTTCGATTCCCTGGGGAACTAGTAGAACATTGAGCTATGGTATGCAACGAAATCAGGATAATGAGATTTCGCATACTGCTTCGTGGTATGACTCTTCCGATCGAAATAATTCCTGGAGCGTTTCTGCTGCAGGCGACAATGATGAATTCaa                                                <  1:123524/251‑1 (MQ=255)                                                                                                                                                                                                                       tAAAAAACGTCTCCACTTCTCTAACATTTAGCCTAATAAACTGGGAAGAAGACAACCAGGATCAACTGTACCTAAATATTTCGATTCCCTGGGGAACTAGTAGAACATTGAGCTATGGTATGCAACGAAATCAGGATAATGAGATTTCGCATACTGCTTCGTGGTATGACTCTTCCGATCGAAATAATTCCTGGAGCGTTTCTGCTTCAGGCGACAATGATGAATTCAAAGATATGAAAGCGTCACTAcg                           <  1:56368/250‑1 (MQ=255)                                                                                                                                                                                                                                               catgtAGCCGAATAAACTGGGAAGAAGACAGCCAGGATCAACTGTACCTAAATATTTCGATTCCCTGGGGAGCTAGTAGAACATTGAGCTATGGTATGCAACGAAATCAGGATAATGAGATTTCGCATACTGCTTCGTGGTATGACTCTTCCGATCGAAATAATTCCTGGAGCGTTTCTGCTTCAGGCGACAATGATGAATTCAAAGATATGAAAGCGTTACGACGCGCGAGtgaccattattataccgag  <  1:53709/247‑19 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                  AAAAACTTTGTGACAATGAATGAATATATCAATGACACTAACCATTACACGAATTATCAGAATGAAAAAGAGAGTTATATTGTCACGTTTAACCAGTATCTTGAATCATTAAGGTTAAATACATACGTAAGTTTGGCTCGTAATACTTACTGGGACGCCAGCAGTAATGTGAATTATTCATTATCACTTAGCCGCGATTTTGATATCGGGCCATTAAAAAACGTCTCCACTTCTCTAACATTTAGCCGAATAAACTGGGAAGAAGACAACCAGGATCAACTGTACCTAAATATTTCGATTCCCTGGGGAACTAGTAGAACATTGAGCTATGGTATGCAACGAAATCAGGATAATGAGATTTCGCATACTGCTTCGTGGTATGACTCTTCCGATCGAAATAATTCCTGGAGCGTTTCTGCTTCAGGCGACAATGATGAATTCAAAGATATGAAAGCGTCACTACGCGCCAGTTATCAGCATAATACCGAG  >  NC_000913/3188765‑3189253

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑