Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,383,257	Δ1 bp	10.3%	coding (545/1212 nt)	elaD →	protease ElaD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,383,257	0	C	.	10.3%	128.4 / 8.7	39	coding (545/1212 nt)	elaD	protease ElaD
Reads supporting (aligned to +/- strand):  ref base C (17/18);  new base . (2/2);  total (19/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.30e-01

CCAACTCCCCCCTCAAATCACATGATTCAGATGATCTCCTGTTCAAAAAACTATTCTCCCCTTCGAAATTAATGACAATTATCGGTGATGAAATTCCTCTTATATCTGAAAAACAGTCGCTTTCAAAGGTGCTTTTAAATGATGAGAATAATGAACTGAGTGATGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTCCCCTACTCCACCAGAACTCACCTGGAAGACGCTCTCAATGAAAATATTAAGAGCGATCCATCATGGCCGAATGAAGTCCAGTTATTCCCCATAAATACTGGCGGACACTGGATATTAGTTTCGCTACAGAAAATAGTAAATAAAAAAAATAATAAACTACAAATAAA  >  NC_000913/2383014‑2383464                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                ccaacTCCCCCTTCAAATCACATGATTCAGATGATCTCCTGTTCAAAAAACTATTCTCCCCTTCGAAATTAATGACAATTATCGGTGATGAAATTCCTCTTATATCTGAAAAACAGTCGCTTTCAAAGGTGCTTTTAAATGATGAGAATAATGAACTGAGTGATGGTATAAACGTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGt                                                                                                                                                                                  <  1:351774/275‑1 (MQ=255)                 aTCACATGATTCAGATGATCTCCTGTTCAAAAAACTATTCTCCCCTTCGAAATTAATGACAATTATCGGTGATGAAATTCCTCTTATATCTGAAAAACAGTCGCTTTCAAAGGTGCTTTTAAATGATGAGAATAATGAACTGAGTGATGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTa                                                                                                                                                                                       <  1:181103/254‑1 (MQ=255)                                         gTTCAAAAAACTATTCTCCCCTTCGAAATTAATGACAATTATCGGTGATGAAATTCCTCTTATATCTGAAAAACAGTCGCTTTCAAAGGTGCTTTTAAATGATGAGAATAATGAACTGAGTGATGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGtctc                                                                                                                                                                               >  2:178295/1‑238 (MQ=255)                                         gTTCAAAAAACTATTCTCCCCTTCGAAATTAATGACAATTATCGGTGATGAAATTCCTCTTATATCTGAAAAACAGTCGCTTTCAAAGGTGCTTTTAAATGATGAGAATAATGAACTGAGTGATGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTACCTACGTCCCCAACCCAACCAAAACACACCTggcaacat                                                                                                                                          >  2:40006/1‑269 (MQ=255)                                             aaaaaaCTATTCTCCCCTTCGAAATTAATGACAATTATCGGTGATGAAATTCCTCTTATATCTGAAAAACAGTCGCTTTCAAAGGTGCTTTTAAATGATGAGAATAATGAACTGAGTGATGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACg                                                                                                                                                                           <  1:178295/238‑1 (MQ=255)                                                                                                 ctctTATATCTGAAAAACAGTCGCTTTCAAAGGTGCTTTTAAATGATGAGAATAATGAACTGAGTGATGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTCCCCTACTCCACCAGAACTCACCTGGAAGACGCTCTCAATGAAAATATTAAGAGCGATCCATCATGGCCGAATGAAGTCCAGTTATTc                                                                                  <  1:40006/275‑1 (MQ=255)                                                                                                                                                        tGAACTGAGTGATGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGt                                                                                                                                                                                  >  2:108556/1‑124 (MQ=255)                                                                                                                                                        tGAACTGAGTGATGGTACAAACTTCTGGGATAAAAATCGTCAATCAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCaaaa                                                                                                                                                                                                             >  1:8423/1‑97 (MQ=255)                                                                                                                                                            cTGAGTGATGGTACAAACTTCTTGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATa                                                                                                                                                                                                         <  2:8423/97‑1 (MQ=255)                                                                                                                                                            cTGAGTGATGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTctct                                                                                                                                                                              <  1:108556/124‑1 (MQ=255)                                                                                                                                                               aGTGATGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAg                                                                                                                                                                                                   >  2:55351/1‑100 (MQ=255)                                                                                                                                                               aGTGATGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAg                                                                                                                                                                                                   >  1:36060/1‑100 (MQ=255)                                                                                                                                                               aGTGATGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTAt                                                                                                                                                                                           >  1:66226/1‑108 (MQ=255)                                                                                                                                                               aGTGATGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATG‑AAAAAATACTCAAGTCAATTAt                                                                                                                                                                                           >  2:18464/1‑107 (MQ=255)                                                                                                                                                                   aTGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCaa                                                                                                                                                                                               <  2:36060/100‑1 (MQ=255)                                                                                                                                                                   aTGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCaa                                                                                                                                                                                               <  1:55351/100‑1 (MQ=255)                                                                                                                                                                   aTGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTa                                                                                                                                                                                       <  2:66226/108‑1 (MQ=255)                                                                                                                                                                   aTGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATG‑AAAAAATACTCAAGTCAATTATCCTa                                                                                                                                                                                       <  1:18464/107‑1 (MQ=255)                                                                                                                                                                    tGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATG‑AAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGt                                                                                                                                                                          >  2:190205/1‑119 (MQ=255)                                                                                                                                                                        aCAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATG‑AAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTcccc                                                                                                                                                                      <  1:190205/119‑1 (MQ=255)                                                                                                                                                                         cAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATAc                                                                                                                                                                                                        >  1:99586/1‑85 (MQ=255)                                                                                                                                                                             cTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCaa                                                                                                                                                                                                    <  2:99586/85‑1 (MQ=255)                                                                                                                                                                                 tGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTCCCCTACTCCACCAGAACTCACCTGGAAGACGCTCTCAATGAAAATATTAAGAGCGATCCATCATGGCCGaa                                                                                                  >  1:227619/1‑179 (MQ=255)                                                                                                                                                                                 tGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTCCCCTACTCCACCAGAACTCACCTGGAAGACGCTCTCAATGAAAATATTAAGAGCGATCCATCATGGCCGAATGAAGTCCAGTTATTCCCCATAAATACTGGCGGACACTGGATATTAGTTTCGCTACAGAAAATAGTAAATAAAAAAAATAATAAACTACAAATaaa  >  1:128808/1‑275 (MQ=255)                                                                                                                                                                                     aTAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTCCCCTACTCCACCAGAACTCACCTGGAAGACGCTCTCAATGAAAATATTAAGAGCGATCCATCATGGCCGAATGaa                                                                                              <  2:227619/179‑1 (MQ=255)                                                                                                                                                                                             cGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTg                                                                                                                                                                                    >  1:198428/1‑85 (MQ=255)                                                                                                                                                                                              gTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTAt                                                                                                                                                                                           >  1:168260/1‑77 (MQ=255)                                                                                                                                                                                                 aaTTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGtct                                                                                                                                                                                <  2:198428/85‑1 (MQ=255)                                                                                                                                                                                                  aTTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTa                                                                                                                                                                                       <  2:168260/77‑1 (MQ=255)                                                                                                                                                                                                             aTGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGt                                                                                                                                                                          >  2:189088/1‑79 (MQ=255)                                                                                                                                                                                                                 aaTAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTcccc                                                                                                                                                                      <  1:189088/79‑1 (MQ=255)                                                                                                                                                                                                                 aaTAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTCCCCTACTccacc                                                                                                                                                             >  1:240365/1‑88 (MQ=255)                                                                                                                                                                                                                     gCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTCCCCTACTCCACCAGaa                                                                                                                                                         <  2:240365/88‑1 (MQ=255)                                                                                                                                                                                                                     gCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTCCCCTACTCCACCAGAACTCACCTGGAAGACGCTCTCAATGAAAATATTAAGAGCGATCCATCATGGCCGAATGAAGTCCAGTTATTCCCCATAAATACTGGCg                                                                  >  1:126291/1‑175 (MQ=255)                                                                                                                                                                                                                         gCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTCCCCTACTCCACCAGAACTCACCTGGAAGACGCTCTCAATGAAAATATTAAGAGCGATCCATCATGGCCGAATGAAGTCCAGTTATTCCCCATAAATACTGGCGGaca                                                              <  2:126291/175‑1 (MQ=255)                                                                                                                                                                                                                                       aTCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTCCCCTACTCCACCAGAACTCACCTGGAAGACGCTCTCAATGAAAATATTAAGAGCGATCCATCATGGCCGAATGAAGTCCAGTTATTCCCCATAAATACTGGCGGACACTGGATATTAGttt                                                >  1:345321/1‑175 (MQ=255)                                                                                                                                                                                                                                         cgccgcTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTCCCCTACTCCACCAGAACTCACCTGGAAGACGCTCTCAATGAAAATATTAaga                                                                                                                     >  2:84544/1‑104 (MQ=255)                                                                                                                                                                                                                                           ccgcTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTCCCCTACTCCACCAGAACTCACCTGGAAGACGCTCTCAATGAAAATATTAAGAGCGATCCATCATGGCCGAATGAAGTCCAGTTATTCCCCATAAATACTGGCGGACACTGGATATTAGTTTCGCt                                            <  2:345321/175‑1 (MQ=255)                                                                                                                                                                                                                                             gcTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTTCGTCCCCTACTCCACCAGAACTCACCTGGAAGACGCTCTCAATGAAAATATTAAGAGCGa                                                                                                                 <  1:84544/104‑1 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                CCAACTCCCCCCTCAAATCACATGATTCAGATGATCTCCTGTTCAAAAAACTATTCTCCCCTTCGAAATTAATGACAATTATCGGTGATGAAATTCCTCTTATATCTGAAAAACAGTCGCTTTCAAAGGTGCTTTTAAATGATGAGAATAATGAACTGAGTGATGGTACAAACTTCTGGGATAAAAATCGTCAATTAACCACAGATGAAATAGCTTGCTATCTTCAGAAGATCGCCGCTAATGCAAAAAATACTCAAGTCAATTATCCTACTGGTCTCTACGTCCCCTACTCCACCAGAACTCACCTGGAAGACGCTCTCAATGAAAATATTAAGAGCGATCCATCATGGCCGAATGAAGTCCAGTTATTCCCCATAAATACTGGCGGACACTGGATATTAGTTTCGCTACAGAAAATAGTAAATAAAAAAAATAATAAACTACAAATAAA  >  NC_000913/2383014‑2383464

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑