Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,363,972	C→T	13.6%	intergenic (+47/‑27)	adhP → / → PP_3840	alcohol dehydrogenase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,363,972	0	C	T	13.6%	104.4 / 7.5	44	intergenic (+47/‑27)	adhP/PP_3840	alcohol dehydrogenase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (16/22);  new base T (3/3);  total (19/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.76e-01

CCCAAGGTAACGCTGCGACCGATCGAGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGACAAGCATTACCGCAACACGCAGAAGGTTCGTCAGTTTCTGCTCAGC  >  NC_002947/4363824‑4364112                                                                                                                                                     |                                                                                                                                             cccAAGGTAACGCTGCGACCGATCGAGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGAc                                                                                                                                              >  7:187708/1‑149 (MQ=255)            gCTGCGACCGATCGAGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGc                                                                                                                                   >  4:239825/1‑149 (MQ=255)                cGACCGATCGAGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCtttt                                                                                                                               <  4:149890/149‑1 (MQ=255)                cGACCGATCGAGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCttt                                                                                                                                <  3:239825/148‑1 (MQ=255)                cGACCGATCGAGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGCAGAGGGTCATCTACGGGCtttg                                                                                                                               <  3:190504/149‑2 (MQ=255)                cGACCGATCGAGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGCAGAGGGTCATCTACGGGCtt                                                                                                                                 <  5:53668/147‑1 (MQ=255)                 gACCGATCGAGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTa                                                                                                                              <  8:55195/149‑1 (MQ=255)                 gACCGATCGAGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGACGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTa                                                                                                                              >  3:206761/1‑149 (MQ=255)                   ccGATCGAGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGCAGAGGGTCATCTACGGGCtttaga                                                                                                                             >  1:107123/1‑145 (MQ=255)                   ccGATCGAGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGCAGAGGGTCATCTACGGGCtt                                                                                                                                 <  2:107123/144‑1 (MQ=255)                     gATCGAGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCct                                                                                                                          >  2:234658/1‑149 (MQ=255)                       tCGAGGGTATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCcttc                                                                                                                        <  4:271213/149‑1 (MQ=255)                       tCGAGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCcttc                                                                                                                        <  6:247331/149‑1 (MQ=255)                          aGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCcttctt                                                                                                                      >  6:226106/1‑148 (MQ=255)                             atatCAACCAGATCTTTGACGAGATGCTGTAGGGCAAGTTCAAAGGCCGGATGGTGATACAGTTCGACGGCTGACAGGCCGAGCCATGTCATGTGGAACCTCAGCAAAGCCCGTAGTTGACCCTCTGCGGGCTTTTAGCCTTCTTAAtt                                                                                                                  <  8:192996/149‑1 (MQ=255)                             atatCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAAtt                                                                                                                  <  8:187708/149‑1 (MQ=255)                             atatCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAAtt                                                                                                                  >  6:48940/1‑149 (MQ=255)                                tCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTc                                                                                                               <  4:206761/149‑1 (MQ=255)                                   aCCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCaaa                                                                                                            <  2:223249/149‑1 (MQ=255)                                   aCCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCa                                                                                                              >  3:156680/1‑147 (MQ=255)                                          cTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCct                                                                                                                                           >  6:86302/1‑111 (MQ=255)                                          cTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCct                                                                                                                                           <  5:86302/111‑1 (MQ=255)                                            ttGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACGGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGAc                                                                                                   >  1:218009/1‑149 (MQ=255)                                             tGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACa                                                                                                      <  5:48940/145‑1 (MQ=255)                                               aCGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCa                                                                                                 <  4:202108/148‑1 (MQ=255)                                                       cTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTc                                                                                         <  1:80756/148‑1 (MQ=255)                                                           aGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTg                                                                                    <  4:184283/149‑1 (MQ=255)                                                                      aaaGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTCCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGc                                                                         >  7:220235/1‑149 (MQ=255)                                                                          gCCGGATGTTTATACAGTTCGAAGGCTGTCAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGAt                                                                     <  8:220235/149‑1 (MQ=255)                                                                                   tGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCAGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGACGACAGGCACGCCCGGCCGATTAGCCGCAc                                                            >  4:92376/1‑149 (MQ=255)                                                                                           ttCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCTCAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCAc                                                    <  5:269079/149‑1 (MQ=255)                                                                                                 ggCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGAc                                               >  3:30393/1‑148 (MQ=255)                                                                                                    tGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGACAAg                                            >  7:79054/1‑148 (MQ=255)                                                                                                          gCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGACAAGCATTAcc                                     >  8:184354/1‑149 (MQ=255)                                                                                                          gCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGACAAGCATTAcc                                     <  5:226106/149‑1 (MQ=255)                                                                                                          gCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGACAAGCATTAcc                                     <  2:218009/149‑1 (MQ=255)                                                                                                             gAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGACAAGCATTACCGCa                                  <  8:79054/149‑1 (MQ=255)                                                                                                                     tCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGACAAGCATTACCGCAACACg                             >  5:265822/1‑146 (MQ=255)                                                                                                                                cacaGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGACAAGCATTACCGCAACACGCAGAAGGTTCGTCa               <  3:92376/149‑1 (MQ=255)                                                                                                                                    taaaaGCCCGAAGAGGGTCATCTACGGGCATTTACCCTTCTTAATTGTCAAAGGAACAGACCATGACCGACGACAGCCACGCCGGGCAGATTAGCCGAACTACAACACTGGACAACAATAACCGAAACAAGCAGAATGATCGTCACtt            >  8:131037/3‑148 (MQ=255)                                                                                                                                     cAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGACAAGCATTACCGCAACACGCAGAAGGTTCGTCAGTTTc          <  5:130186/149‑1 (MQ=255)                                                                                                                                     aaaaGCCCGCAGAGGGTCATCTACGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGACAAGCATTACCGCAACACGCAGAAGGTTCGTCAGTTTc          >  5:32998/2‑149 (MQ=255)                                                                                                                                            cGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGACAAGCATTACCGCAACACGCAGAAGGTTCGTCAGttt           >  4:77767/1‑141 (MQ=255)                                                                                                                                            cGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGACAAGCATTACCGCAACACGCAGAAGGTTCGTCAGttt           <  3:77767/141‑1 (MQ=255)                                                                                                                                               aGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGACAAGCATTACCGCAACACGCAGAAGGTTCGTCAGTTTCTGCTCAGc  >  1:124386/1‑147 (MQ=255)                                                                                                                                                     |                                                                                                                                             CCCAAGGTAACGCTGCGACCGATCGAGGATATCAACCAGATCTTTGACGAGATGCTGGAGGGCAAGATCAAAGGCCGGATGGTGATACAGTTCGAAGGCTGACAGGCCGAGCCAGGTCATGTGGAACCACAGCAAAGCCCGTAGATGACCCTCTGCGGGCTTTTAGCCTTCTTAATTGTCAAAGGAACAGACCATGACCGTCGACTGGCACGCCGGGCCGATTAGCCGCACGACTCCACTGGACAAGCATTACCGCAACACGCAGAAGGTTCGTCAGTTTCTGCTCAGC  >  NC_002947/4363824‑4364112

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: ‑