Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,269,969	A→C	8.8%	intergenic (+367/+247)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,269,969	0	A	C	8.8%	149.3 / 4.0	61	intergenic (+367/+247)	yhaC/rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
Reads supporting (aligned to +/- strand):  ref base A (21/32);  new base C (3/3);  total (24/37)
Fisher's exact test for biased strand distribution p-value = 6.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCGGGTTTTTACGTAAACCAGGTGAAAC  >  NC_000913/3269823‑3270111                                                                                                                                                   |                                                                                                                                               aaTAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAg                                                                                                                                              >  2:313206/1‑149 (MQ=255)   tAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTATAACCCAACAACAGTAAAAACAAGCCGAATCg                                                                                                                                            >  3:64391/1‑149 (MQ=18)     aaGCGCCCTCCACAATCTTAAACCCGCCGTATCGGTTTATTACGTAAATCAGGTTAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCggg                                                                                                                                          <  2:145260/149‑1 (MQ=14)       gcgcACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACACTGCTTAAGGATTCTGCCCCTGCAAAAGTAAAAAACCCCCGAAGCGGGtg                                                                                                                                        >  7:136660/1‑148 (MQ=18)            cTCCACCATCTGACCCCCGCCGGCACGGGGTATTACGTACCTCCGGTACCACGGCCCGATACGCCGCTGTCTTTTGGGGATAGGGTCGTGGACAGGCATTCCTCTTTCTGCCCCTCCAAAAGTAACCACCCGCTTCGGCGGGTTTTTAc                                                                                                                                   <  1:380779/149‑1 (MQ=9)            cTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTAc                                                                                                                                   <  8:320179/149‑1 (MQ=255)            cTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGCTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTAc                                                                                                                                   <  3:671/149‑1 (MQ=255)             tCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTAAATCATAATTCAGCCCGTCAAAAATAAAAAAACCGAAGAGGCGGTTTTTTTCg                                                                                                                                  >  5:383178/1‑149 (MQ=17)              caacaaTCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGt                                                                                                                                 <  1:313206/149‑1 (MQ=255)               aacaaTCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTa                                                                                                                                <  8:123796/149‑1 (MQ=255)                 caaTCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCGGTCTTTTGGGTATAGTGTCGTGGCCAGGCATTCATCGTTCGGCCGCTCCAAAAGAAAAAACCCGCCGCAGCGGGTTTTTACGGaaa                                                                                                                              >  1:156695/1‑149 (MQ=17)                   aTCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCAGCGCCTACAAAAGTAAAAACCCGCAGCAGGGCGTATTTAccttata                                                                                                                             >  1:14568/1‑142 (MQ=17)                     cTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAg                                                                                                                          >  6:82701/1‑149 (MQ=255)                       gAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGt                                                                                                                        >  2:11042/1‑149 (MQ=255)                        aaaCCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAgg                                                                                                                         <  2:43668/147‑1 (MQ=255)                        aaaCCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAg                                                                                                                          <  4:338094/146‑1 (MQ=255)                        aaaCCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAg                                                                                                                          <  7:137921/146‑1 (MQ=255)                        aaaCCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAg                                                                                                                          <  8:292016/146‑1 (MQ=255)                        aaaCCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTg                                                                                                                       <  5:82701/149‑1 (MQ=255)                          aCCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGaa                                                                                                                     <  1:11042/149‑1 (MQ=255)                           cccGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGaaa                                                                                                                    <  7:32473/149‑1 (MQ=255)                           cccGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGaaa                                                                                                                    <  1:272023/149‑1 (MQ=255)                            ctgccgGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTAGTGGACAGTCATTAATCTTTCTGCCCCTCCAAAAGAAAAAACCCGCCGAAGCGGGTTTTTACGTAAACCAGGTGaaa                                                                                                                    >  5:66929/3‑148 (MQ=255)                               ccgGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGa                                                                                                                <  1:213200/149‑1 (MQ=255)                               ccgGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGa                                                                                                                <  6:222882/149‑1 (MQ=255)                               ccgGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGa                                                                                                                <  2:107269/149‑1 (MQ=255)                                 ggAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGAcc                                                                                                              <  3:3933/149‑1 (MQ=255)                                      ggTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATaa                                                                                                         <  6:103715/149‑1 (MQ=255)                                               cttACATTAGGTAATACTGTCCGATAATCCGAATTCTTTTTGTTCTATTGTCGAGGAAAGTGATTCTTCTTTCTGCCACTCCAAAATATAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGctttc                                                                                                <  1:365807/147‑1 (MQ=11)                                                   cATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGttt                                                                                                                                       >  6:215475/1‑106 (MQ=40)                                                   cATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGttt                                                                                                                                       <  5:215475/106‑1 (MQ=40)                                                     tCAGGTATAACTCACCGATAATCCGATTTCTTTTGTGTCTAGTCTATGTGTCAGTCATTCAGATTTATGGCACTCAAAAATTTAAAACCCGCCGTATCGGGTTTTTACGTAAAACAGGTTAAACTGACCGATAAGCCGCTTTCTTTTgg                                                                                          <  8:136660/149‑1 (MQ=2)                                                            aatccttccGATATGCCCATTTGTTATGGGATTTGTGTCGTGGACTGTTATTATATTTTCTGCCCCTCCACAATCAGAAACCCGCCGAATCGGGTTTTTACGTAAAACAGGTCAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAgt                                                                                   <  1:286977/142‑1 (MQ=2)                                                                tGACCTATAAGCCGCTTTCTTTTTGGTATAGTGTCGTGGAGAGTCATTCATCTTTCTGCGCCTCGAAAAGTAAAAACCCGCGGAAGCGGGTTTTTACGTAATAGAGGTGAATCTGACCGATa                                                                                                          <  6:376385/122‑1 (MQ=11)                                                                tGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTTCCCCTCCAAAAGTAAAAACCCGCCGAATCGTGTTTTTACGTAAAACAAGTGAAACTGACCGATa                                                                                                          >  5:376385/1‑122 (MQ=255)                                                                      aTAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAg                                                                                                                          >  1:230618/1‑100 (MQ=37)                                                                      aTAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAg                                                                                                                          <  2:230618/100‑1 (MQ=37)                                                                          gCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAg                                                                                                                          <  7:80140/96‑1 (MQ=37)                                                                          gCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGAAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAg                                                                                                                          >  8:80140/1‑96 (MQ=18)                                                                              ctttctttTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGAAAAGCCGCTTTCtctt                                                                                            <  4:367636/122‑1 (MQ=25)                                                                              ctttctttTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGAAAAGCCGCTTTCtctt                                                                                            >  3:367636/1‑122 (MQ=25)                                                                                             aGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGctttcttt                                                                                             <  2:214800/106‑1 (MQ=35)                                                                                                   gTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCtttt                                                                                            >  2:268837/1‑101 (MQ=35)                                                                                                   gTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCtttt                                                                                            <  1:268837/101‑1 (MQ=35)                                                                                                             attcatCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGCGTCGTg                                                                             <  2:174167/106‑1 (MQ=17)                                                                                                             attcatCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGCGTCGTg                                                                             >  1:174167/1‑106 (MQ=17)                                                                                                                    tttCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGtata                                                                                     >  1:372476/1‑91 (MQ=37)                                                                                                                          ccccTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGtat                                                                                      >  1:308308/1‑84 (MQ=38)                                                                                                                           cccTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTCTCTTTTGGGTATAgtg                                                                                  <  8:218897/87‑1 (MQ=255)                                                                                                                           cccTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTCTCTTTTGGGTATAgtg                                                                                  >  7:218897/1‑87 (MQ=255)                                                                                                                              tCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGctt                                                                                                  >  8:199756/1‑68 (MQ=40)                                                                                                                               ccAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAAACCGCCGAAGCGGGTTTTTACg                 >  6:261533/1‑148 (MQ=37)                                                                                                                                cAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATa                                                                                                          >  8:190339/1‑58 (MQ=255)                                                                                                                                cAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATa                                                                                                          <  7:190339/58‑1 (MQ=255)                                                                                                                                 aaaaGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGCGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCaaaa                                              >  3:14494/1‑117 (MQ=17)                                                                                                                                 aaaaGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGCGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCaaaa                                              <  4:14494/117‑1 (MQ=17)                                                                                                                                   aatgacaaaCCCGCCGTATCGGGTTTTTACGTAAAACAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCGGGTTTTTACGTAAAc            <  3:226072/143‑1 (MQ=11)                                                                                                                                      tAAAAACCCGCTTCGGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCttt                                                            <  6:369810/98‑1 (MQ=11)                                                                                                                                      tAAAAACCCGCTTCGGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCttt                                                            >  5:369810/1‑98 (MQ=11)                                                                                                                                            cctgccgCACCGGTTTTTTACGTAAATCAGGTTAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCGGGTTTTTACGTAAACCAGGTGaaa   <  6:66929/146‑1 (MQ=11)                                                                                                                                             ccgccgAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCGGGTTTTTACGTAAACCAGGTGAAAc  <  5:261533/149‑1 (MQ=37)                                                                                                                                                   |                                                                                                                                               AATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCGGGTTTTTACGTAAACCAGGTGAAAC  >  NC_000913/3269823‑3270111

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑