Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_hsa_pgi	526,792	A→C	24.9%	S1178R (AGC→CGC)	rhsD →	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_hsa_pgi	526,792	0	A	C	24.9%	82.6 / 18.0	49	S1178R (AGC→CGC)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
Reads supporting (aligned to +/- strand):  ref base A (16/20);  new base C (8/5);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 3.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAATCAGGGCTGTACTATAACCGTCACCGGTACTACGATCC  >  NC_000913_3_hsa_pgi/526649‑526928                                                                                                                                                |                                                                                                                                         ttGCGCAGTGCGGGCTGACGGTAGAGCAAATGGCAAGACAGGTGGGGACGGAATACACACCGGCACGAAAAGCTCATCTGTATAACTGCGACCAGCGGGCACAGCCGCCGGGGCGTATTAGCAAACGCGACAAAACGGAGCGGcgcgag                                                                                                                                     >  2:217946/1‑147 (MQ=9) ttGCGCAGTGCGGGCTGACGGGGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGcgcggg                                                                                                                                     <  1:563841/149‑3 (MQ=255)    cgcAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAACGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGTGCGGac                                                                                                                                  >  1:601803/1‑148 (MQ=255)    cgcAGTGCGGGCGGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTAGCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGaa                                                                                                                                  <  2:347484/149‑1 (MQ=255)         tGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGTGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTatga                                                                                                                             <  1:631026/149‑1 (MQ=11)          gCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCCCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATatgat                                                                                                                            <  1:84624/149‑1 (MQ=255)             ggCTCACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTTGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGaa                                                                                                                         <  1:67099/149‑1 (MQ=11)                    ggTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGATGAGCTCATCGTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCa                                                                                                                  <  2:537408/149‑1 (MQ=11)                         ggcagggggCCAGACAGGTGGAGCCGTAATACACGCCGGCGTGAAAATGTCATCTATTTCACTGCCACCCCCGGAGACTTCCGCTGGCGCTTATCAGCGGAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAg                                                                                                             <  2:144615/142‑1 (MQ=14)                               tGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAAt                                                                                                       <  1:353366/149‑1 (MQ=255)                                ggCCAGACAGGTGGGGCCGGAATACACACCGGCGCGAAAAGCTCTTCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATg                                                                                                      <  2:220413/149‑1 (MQ=255)                                   cAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGAGCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACAAGCTTAATgagg                                                                                                   >  1:442682/1‑149 (MQ=11)                                   cAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATgagg                                                                                                   <  1:398431/149‑1 (MQ=255)                                      aCAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGgaga                                                                                                >  1:448301/1‑149 (MQ=255)                                      aCAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCCTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGgaga                                                                                                >  1:290416/1‑149 (MQ=255)                                        aGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAAc                                                                                              >  1:386872/1‑149 (MQ=255)                                          gTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGACGCCGGCAATACGGCGTGGCGCGGGGAGTACGATGCATGGCGCAACACGCTTAACGAGGCGCAccc                                                                                            >  1:471000/1‑149 (MQ=11)                                             gggCCGGAACACAACTCGGCGCGAAAAGCTCATCTTTATCACTGCTACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGca                                                                                         <  2:2874/147‑1 (MQ=11)                                              aGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCAGcat                                                                                        >  1:287430/1‑149 (MQ=255)                                               gCCGGAATACGCACCGGCGCGATAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGcatc                                                                                       <  2:620535/149‑1 (MQ=11)                                                ccGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGcatca                                                                                      >  1:43194/1‑149 (MQ=255)                                                 cGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAAGGGGGCAACCGGCTTAATGAGGAGGGCCCGcatacg                                                                                     >  2:550840/1‑146 (MQ=11)                                                  ggAATACACACCGGCGCGAAAAGCTCATCATTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGcatcacc                                                                                    >  1:563565/1‑147 (MQ=11)                                                   gAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGATTAAAGGGGAGAGCCCGcatcccct                                                                                   >  1:438638/1‑145 (MQ=11)                                                   gAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCAtgt                                                                                   <  1:295218/149‑1 (MQ=255)                                                    aaTACACCCCGGCGCGAAAAGCTCAACTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCAtgtg                                                                                  <  1:9956/149‑1 (MQ=255)                                                         acacCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCa                                                                             <  1:334703/149‑1 (MQ=255)                                                           cccGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGc                                                                           <  1:219773/148‑1 (MQ=255)                                                            ccGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATGATGTGTATCAGcc                                                                          <  1:544859/149‑1 (MQ=255)                                                            ccGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGcc                                                                          >  1:115740/1‑149 (MQ=255)                                                                 gcgAAAAGCTCATCTTTATCACTGCGACCACCGGGGGCTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAAGGAGGAGAACCCGCATCATGTGTATCAGCCGTAcc                                                                     >  1:78134/1‑149 (MQ=255)                                                                          tCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAg                                                            >  1:481301/1‑149 (MQ=255)                                                                          tCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTAGAGCGCGGCCTAAGATGAATGGAACAACCAGCTTAATGAGGAGGACCCGCATCCGATGTATGAGCAGTGCCGTCtcgacg                                                            >  2:215539/1‑144 (MQ=17)                                                                          tCATCTTTATCACTGCGACCACCGGGGACTGCCGCCGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGGGGAATATGAGGAGTGGGGCAACCAGCTTGTTGACGCGAACCCGCGTGAGGTGTATCAACCGTGCCGTCCTCCAg                                                            >  2:613186/1‑149 (MQ=17)                                                                          gagtCTTTATCACTGCGCCCAGCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAg                                                            <  2:258117/146‑1 (MQ=255)                                                                            gtttgtgtCATTGCGACCCGCGGGGACGGTCGTTGGCGCTTATCAGCGAAGGCGGCAATACGGCGTGGAGCGGGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAggg                                                          <  2:550473/142‑1 (MQ=17)                                                                                ttACCACTGCGACCACGGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGgcagc                                                      <  2:78134/149‑1 (MQ=255)                                                                                      cTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGAGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCatg                                                >  1:267911/1‑149 (MQ=255)                                                                                          gACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCAtgatga                                            <  1:467707/149‑1 (MQ=255)                                                                                           accaccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCAGGCTGAg                                           >  1:152012/1‑149 (MQ=255)                                                                                                cGGGGACTGCCGCTGGCGCTTATCAGCTAAGACGGCTATACGGGCTAGACAGCTGAATATGATGAATGAGGCAACCAGCTTACTGAGGCGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAATc                                      <  1:188814/149‑1 (MQ=17)                                                                                                 ggggACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAATCa                                     <  1:385468/149‑1 (MQ=255)                                                                                                 ggggACCGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAATCa                                     <  1:356612/149‑1 (MQ=255)                                                                                                  gggACTGCCGCTGGCGCTTATGAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAATCAg                                    <  2:424932/149‑1 (MQ=255)                                                                                                    gACTGCCGCTGGCGCTTATCAGCGAAGACGGCAAGACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAATCAggg                                  <  2:342597/149‑1 (MQ=255)                                                                                                               gcgcTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAATCAGGGCTGTAatatga                       >  1:22584/1‑147 (MQ=255)                                                                                                                   ttATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAATCAGGGCTGTACTATAACCGt                   >  1:202999/1‑149 (MQ=255)                                                                                                                        aGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAATCAGGGCTGTACTATAACCGTCACCg              >  1:256707/1‑149 (MQ=255)                                                                                                                                 ggCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCCGCTTCATGAGGGGAACCCGAATCAGGTGTATCAGCCATCCCGACTGCCCGGGCACCAGCATGATGAGGAATCAGAGCTGTTCTATTCCCGTAACAGGtcgtatgc     >  2:102762/1‑142 (MQ=17)                                                                                                                                 ggCAATACGGAGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAATCAGGGCTGTACTATGACCGTCACCGGtcctcagg     >  1:649532/1‑145 (MQ=255)                                                                                                                                    aaTACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAATCAGGGCTGTACTATAACCGTCACCGGTACTACGATcc  >  1:337610/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                         TTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGAGCGCGGAATATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCATGTGTATCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAATCAGGGCTGTACTATAACCGTCACCGGTACTACGATCC  >  NC_000913_3_hsa_pgi/526649‑526928

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑