Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,484,724	A→T	8.7%	intergenic (+368/‑101)	PP_3976 → / → PP_3977	isochorismatase family hydrolase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,484,724	0	A	T	8.7%	131.0 / 3.4	46	intergenic (+368/‑101)	PP_3976/PP_3977	isochorismatase family hydrolase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (21/21);  new base T (2/2);  total (23/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

GGCTCAAACCCTGGCAGGTCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGCAAAACCGGGTCTTCCGCGCAAGCTTCAG  >  NC_002947/4484577‑4484869                                                                                                                                                    |                                                                                                                                                  ggcTCAAACCCTGGCAGGTCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGaa                                                                                                                                                   >  1:244843/1‑148 (MQ=255) ggcTCAAACCCTGGCAGGTCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGaa                                                                                                                                                   <  2:244843/148‑1 (MQ=255)    tCAAACCCTGGCAGGTCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCCGaataa                                                                                                                                                >  3:15501/1‑148 (MQ=255)      aaaCCCTGGCAGGTCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGaataat                                                                                                                                               >  7:23635/1‑147 (MQ=255)        aCCCTGGCAGGTCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAgg                                                                                                                                           >  5:228019/1‑149 (MQ=255)          ccTGGCAGGTCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGATTATTCAGGGc                                                                                                                                         <  2:224767/149‑1 (MQ=255)            tGGCAGGTCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATc                                                                                                                                              >  3:112887/1‑142 (MQ=255)            tGGCAGGTCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATc                                                                                                                                              <  4:112887/142‑1 (MQ=255)            tGGCAGGTCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCtt                                                                                                                                       >  5:67349/1‑149 (MQ=255)              gCAGGTCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCttt                                                                                                                                      <  7:102528/148‑1 (MQ=255)               cAGGTCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAATGCCCTGAATAATCAGGGCTTTGa                                                                                                                                    <  4:78578/149‑1 (MQ=255)                 ggTCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAat                                                                                                                                  <  3:231807/149‑1 (MQ=255)                   tCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGATTATTCAGGGCttttt                                                                                                                                    >  5:168714/1‑143 (MQ=255)                   tCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGATTATTCAGGGCttttt                                                                                                                                    <  6:168714/145‑3 (MQ=255)                               accAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATCAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATCATCAGGGCTTTGAATATGGCGGAAGCGTa                                                                                                                    <  5:264083/147‑1 (MQ=255)                                gCAGATGATGTTGGTGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGACCTGAATAATCAGGGCTTTGAATATGGCGGAAGCg                                                                                                                      >  5:150930/1‑146 (MQ=255)                                            ggAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAAcc                                                                                                        <  8:23635/148‑1 (MQ=255)                                            ggAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGATTTGa                                                                                                                                    >  5:224268/1‑120 (MQ=255)                                            ggAGGCATATCGGTCAAATCATGAGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCAAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGa                                                                                                                                    <  6:224268/120‑1 (MQ=38)                                                     tCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAg                                                                                              <  6:228019/149‑1 (MQ=255)                                                             aGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTcctac                                                                                      <  6:67349/149‑1 (MQ=255)                                                             aGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTcctac                                                                                      >  1:47458/1‑149 (MQ=255)                                                                              agagAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCt                                                                     <  1:1197/149‑1 (MQ=255)                                                                                  aaaTGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACa                                                                                 >  6:209946/1‑133 (MQ=255)                                                                                  aaaTGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACa                                                                                 <  5:209946/133‑1 (MQ=255)                                                                                  aaaTGCGGGCGGTATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATc                                                                 <  7:99693/149‑1 (MQ=255)                                                                                   aaTGCGGGCGTGATCAGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCCGAATAATCATGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATc                                                                 <  4:15501/148‑1 (MQ=255)                                                                                                   gTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCtt                                                >  4:17219/1‑149 (MQ=255)                                                                                                    tATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGc                                                                                            <  1:234141/104‑1 (MQ=255)                                                                                                    tATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGc                                                                                            >  2:234141/1‑104 (MQ=255)                                                                                                          aaGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGAc                                         <  3:95666/149‑1 (MQ=255)                                                                                                             ggTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTc                                                   >  4:57635/1‑136 (MQ=255)                                                                                                             ggTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTc                                                   <  3:57635/136‑1 (MQ=255)                                                                                                              gTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTa                                                             <  3:139976/125‑1 (MQ=255)                                                                                                              gTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTa                                                             >  4:139976/1‑125 (MQ=255)                                                                                                                  aaaaTCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGc                                  >  3:171931/1‑148 (MQ=255)                                                                                                                      tCGGAGCCCCAAAAACGCAAAATGCCCTGAATAATCAGGGCTTTGAATATGGCAGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGc                              >  7:167477/1‑148 (MQ=255)                                                                                                                      tCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGc                              >  2:248000/1‑148 (MQ=255)                                                                                                                             cccAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGCAAAACCgg                      <  3:17219/149‑1 (MQ=255)                                                                                                                             cccAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGCAAAACCgg                      >  3:108831/1‑149 (MQ=255)                                                                                                                             cccAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGCAAAACCgg                      <  2:47458/149‑1 (MQ=255)                                                                                                                             cccAAAAACGCAAAAAGCACTGAATAATCATGGCTTTGAATATGTCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGAATTAATTTCTGTTCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGCAAAACCg                       <  6:150930/148‑1 (MQ=255)                                                                                                                                 aaaaCGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACATAATTTCTGATCGCTAGCTCGAAGTCCTTTATGCACTGTTAGCTAGCAAAACAGGGTc                   >  3:71486/1‑148 (MQ=37)                                                                                                                                        aaaaaGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGCAAAACCGGGTCTTCcgcg            >  4:133591/1‑148 (MQ=255)                                                                                                                                        aaaaaGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGCAAAACCGGGTCTTCcgcg            >  8:234382/1‑148 (MQ=255)                                                                                                                                          aaaGCCCTGATTATTCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGCAAAACAGGGTCTTCCgcgc           >  5:223710/1‑147 (MQ=255)                                                                                                                                              cccTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGCAAAACCGGGTCTTCCGCGCAAGCt      >  3:254406/1‑148 (MQ=255)                                                                                                                                                 tGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGCAAAACCgg                      <  1:203353/129‑1 (MQ=255)                                                                                                                                                 tGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGCAAAACCgg                      >  2:203353/1‑129 (MQ=255)                                                                                                                                                  gAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGCAAAACCGGGTCTTCCGCGCAAGCTTCAg  >  6:169368/1‑148 (MQ=255)                                                                                                                                                   aataatCAGGGCTTTGAATATGGCAGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGCAAAACCGGGTCTTCCGCGCAAGCTTCAg  <  8:167477/147‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                  GGCTCAAACCCTGGCAGGTCGCAACGGCCAAGCAGATGATGTTGGAGGCATATCGGTCACAGCATGCGGAAATGAACAGAGAAATGCGGGCGTGATCCGTATGACAAGGGTAGAAAATCGGAGCCCCAAAAACGCAAAAAGCCCTGAATAATCAGGGCTTTGAATATGGCGGAAGCGTAGAGATTCAAACCCTTATCCTAGGCTCCTACCTACAGACTTAATTTCTGATCGGTAGCTCGACGTCCTTTATGGACTGTAAGCTAGCAAAACCGGGTCTTCCGCGCAAGCTTCAG  >  NC_002947/4484577‑4484869

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑