Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,490,439	G→A	13.8%	pseudogene (170/258 nt)	yjgX ←	pseudogene fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,490,439	0	G	A	13.8%	66.1 / 4.3	29	pseudogene (170/258 nt)	yjgX	pseudogene fragment
Reads supporting (aligned to +/- strand):  ref base G (13/12);  new base A (2/2);  total (15/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.59e-01

ATCCCTGCGCACACTCTCACCAGTGACAATAACAATCGTATCATATAACGGTGCTCCCGGCTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGTGGTCGCGATGGTGTGTCCGCCAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAA  >  CP009273/4490295‑4490579                                                                                                                                                 |                                                                                                                                             atactcgagcACACTCTCACCCGTGACAATAACAATCGTATCATATAACGGTGCTCCCGGCTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTcc                                                                                                                                          <  1:162511/141‑1 (MQ=255)  tCCCTGCGCACACTCTCACCAGTGACAATAACAATCGTATCATATAACGGTGCTCCCGGCTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTTTCCCCACAACTGTTCCt                                                                                                                                         >  2:107754/1‑149 (MQ=255)                ctcACCAGTGACAATAACAATCGTATCATATAACGGTGCTCCCGGCTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCaa                                                                                                                           <  2:113573/149‑1 (MQ=255)                  cACCAGTGACAATACCAATCGTATCATATAACGGTGCTCCCGGCTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAAGGCTGCATTTCACGTAATGTGTCAGTTGTCCTCACAACTGTTCCTTTAACCATCCGCAATg                                                                                                                         <  1:255183/149‑1 (MQ=255)                        ttaCAATAACAAGCGTATCATATAACGGTGCTTCCGGCTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAAc                                                                                                                   <  2:9222/147‑1 (MQ=255)                             aTAACAATCGTATCATATAACGGTGCTCCCGGCTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTATTCCTTTAACCATCCGCAATGGCCAACGGttt                                                                                                              >  1:330130/1‑149 (MQ=255)                             aTAACAATCGTATCATATAACGGTGCTCCCGGCCGGCTATTCCAGTTGTCAGCCCCGTGCCACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTATTCCTTTAACCATCCGCAATGGCCAACGGttt                                                                                                              >  1:254151/1‑149 (MQ=255)                                aCAATCGTATCATATAACGGTGCTCCCGGCTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCACTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACa                                                                                                           <  2:104139/149‑1 (MQ=255)                                       tATCATATAACGGTGCTCCCGGCTTGATTTTCCAGGTGTTAGCCCCGGGCCACTCTGTTGTTCATAAAGCTGCATTTCACGTAATTTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCata                                                                                                    <  1:157698/149‑1 (MQ=255)                                            tatcatggTGCTCCGCGCTGGATTTTCCAGCTGTCAGCCCCTTGCTACGCAGGTCTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTGTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACg                                                                                               <  1:100690/143‑1 (MQ=255)                                            tataACGGTGCTCCCGGTTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACg                                                                                               <  1:52140/149‑1 (MQ=255)                                            tataACGGTGCTCCCGGCTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACg                                                                                               <  1:52144/149‑1 (MQ=255)                                             ataACGGTGCTCCCGGCTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATCATACGa                                                                                              >  2:40320/1‑149 (MQ=255)                                                        cccGGCTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTaga                                                                                   >  2:332276/1‑149 (MQ=255)                                                         ccGGCTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCCTAATACGAATCGCCGTagag                                                                                  >  1:279060/1‑149 (MQ=255)                                                          cGGCTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGagc                                                                                 >  1:152532/1‑149 (MQ=255)                                                                gATTTTCCAGTTGTGACCCCCGTGTTACTCAGTTGTTCATAACGCTGCATTTCACGTAAGGGGTCAGTTGTCCCCACAACTGTTCCTGTAACCATCCGCTATGGCCAACGGTTTACAGAGCATAGTACGAATAGCCGTAGAgccagcca                                                                           <  1:2351/149‑1 (MQ=255)                                                                gATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAgccagcca                                                                           >  2:137708/1‑149 (MQ=255)                                                                               aGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTGGAGCCAGCCCGTTACGGTGGTcgcg                                                            >  1:102248/1‑149 (MQ=255)                                                                                  cccGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGTGGTCGCGATg                                                         >  2:221879/1‑149 (MQ=255)                                                                                    cGTGCTACCCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGTGGTCGCGATGgt                                                       <  2:91366/149‑1 (MQ=255)                                                                                         tACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGTGGTCGGGATGgtaagtc                                                  >  1:177484/1‑144 (MQ=255)                                                                                         tACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGGGGTCGCGATGGTGTGTc                                                  >  2:310713/1‑149 (MQ=255)                                                                                                  gttCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGTGGTCGCGATGGTGTGTCCGCCAGaaa                                         >  1:334667/1‑149 (MQ=255)                                                                                                       tAACGTTGCATTTCACGTAATGTGTCAGTTGGCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGTGGTCGCGATGGTGTGTCCGCCAGAAAATcac                                    <  2:153509/149‑1 (MQ=255)                                                                                                          cGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTATTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGTGGTCGCGATGGTGTGTCCGCCAGAAAATcaccac                                 <  2:254151/149‑1 (MQ=255)                                                                                                          cGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTATTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGTGGTCGCGATGGTGTGTCCGCCAGAAAATcaccac                                 <  2:330130/149‑1 (MQ=255)                                                                                                                                       ccccACAACTGTTCCTTTAACCATTCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGTGGTCGCGATGGTGTGTCCGCCAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGaa    >  2:266231/1‑149 (MQ=255)                                                                                                                                         ccACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGTGGTCGCGATGGTGTGTCCGCCAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGaaaa  >  2:268681/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                             ATCCCTGCGCACACTCTCACCAGTGACAATAACAATCGTATCATATAACGGTGCTCCCGGCTGGATTTTCCAGTTGTCAGCCCCGTGCTACTCAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGTGGTCGCGATGGTGTGTCCGCCAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAA  >  CP009273/4490295‑4490579

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑