Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,905,504	Δ1 bp	7.4%	intergenic (‑98/+30)	PP_4313 ← / ← PP_4314	peptidylprolyl isomerase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,905,504	0	G	.	7.4%	169.7 / 7.3	54	intergenic (‑98/+30)	PP_4313/PP_4314	peptidylprolyl isomerase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (20/30);  new base . (2/2);  total (22/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.09e-01

CGTCTCCCTCGACCAGGTCGATGATCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCTGATTGGCGAAGCAGTACCACGCGGGTTTCTCTTCGACGAAGATCTGCAGGTCGAAATCCCAGGCTTGGTCGC  >  NC_002947/4905364‑4905652                                                                                                                                                |                                                                                                                                                     cGTCTCCCTCGACCAGGTCGATGATCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAATAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCt                                                                                                                                              <  4:60184/149‑1 (MQ=255)   tctcCCTCGACCAGGTCGATGATCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTcc                                                                                                                                            <  3:9033/149‑1 (MQ=255)    ctcCCTCGACCAGGTCGATGATCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCg                                                                                                                                           >  1:98201/1‑149 (MQ=255)       ccTCGACCATCGCGAAGATCTGCAGTTCTTGGCTCTCGCCCCATACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATTCCGTCGGC‑GAATGCCTcc                                                                                                                                            <  1:316103/146‑1 (MQ=255)       ccTCGACCAGGTCGATGATCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTa                                                                                                                                         >  3:358196/1‑148 (MQ=255)       ccTCGACCAGGTCGATGATCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTa                                                                                                                                         >  2:98282/1‑148 (MQ=255)       ccTCGACCAGGTCGATGATCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTa                                                                                                                                         >  4:82896/1‑148 (MQ=255)        cTCGACCAGGTCGATGATCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACa                                                                                                                                       <  3:192223/149‑1 (MQ=255)           gACCAGGTCGATGATCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGa                                                                                                                                     <  4:67822/148‑1 (MQ=255)           gACCAGGTCGATGATCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGAc                                                                                                                                    <  5:354117/149‑1 (MQ=255)             ccAGGTCGATGATCTGCAGTTATTGGCTCACT‑GGTAAAATCCAAACGCTTAAAAACAAAACCGACCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGAAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACAt                                                                                                                                  <  1:238174/149‑1 (MQ=255)                    gatgatCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTg                                                                                                                           <  4:137042/149‑1 (MQ=255)                     attatCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAATCCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGa                                                                                                                          <  7:329935/146‑1 (MQ=255)                     atgatCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTg                                                                                                                           >  3:193397/1‑148 (MQ=255)                     atgatCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGa                                                                                                                          <  1:98282/149‑1 (MQ=255)                             cAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCa                                                                                                                      <  5:102608/145‑1 (MQ=255)                              aGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCGCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGtt                                                                                                                            <  3:95097/138‑1 (MQ=255)                              aGTTCTTGGCTCACC‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGtt                                                                                                                            >  4:95097/1‑138 (MQ=255)                                    tGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGc                                                                                                            <  3:121990/148‑1 (MQ=255)                                     ggCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGc                                                                                                            <  8:322566/147‑1 (MQ=255)                                            g‑ggTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACAt                                                                                                                                  <  5:1712/118‑1 (MQ=255)                                            g‑ggTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACAt                                                                                                                                  >  6:1712/1‑118 (MQ=255)                                               gTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGATGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACctc                                                                                                 >  4:260800/1‑149 (MQ=255)                                                  cacTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTg                                                                                              <  4:193397/149‑1 (MQ=255)                                                    cTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGc                                                                                            <  5:271642/149‑1 (MQ=255)                                                    cTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGc                                                                                            <  1:206016/149‑1 (MQ=255)                                                    cTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGc                                                                                            >  3:147982/1‑149 (MQ=255)                                                       cAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTGACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGCCGTTGATTCAGCTGTTCTGCTCGAACACCTCTTGGCCg                                                                                          >  8:192018/1‑148 (MQ=255)                                                       cAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGcc                                                                                           <  2:98201/147‑1 (MQ=255)                                                        aaaCGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGa                                                                                        <  7:318592/149‑1 (MQ=255)                                                           cGCTGAAAAACAAACCCGCCATTTTCTCAGGAATGCAGCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAg                                                                                     <  4:229919/149‑1 (MQ=255)                                                              tGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATTCCGTCGGC‑GAATGCCTcc                                                                                                                                            <  6:282528/91‑1 (MQ=37)                                                              tGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATTCCGTCGGC‑GAATGCCTcc                                                                                                                                            >  5:282528/1‑91 (MQ=37)                                                                aaaaaCAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTg                                                                                              <  8:216004/135‑1 (MQ=255)                                                                aaaaaCAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTg                                                                                              >  7:216004/1‑135 (MQ=255)                                                                 aaaacaaaacCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTc                                                                                                                                             <  6:358592/87‑1 (MQ=255)                                                                     caaaacCGCCCTTTTCTCAGGAATGCACCGGTTTGCGCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTgg                                                                             >  1:56906/1‑148 (MQ=255)                                                                     caaaacCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGATGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTc                                                                           <  3:260800/149‑1 (MQ=255)                                                                        aacCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCtca                                                                        >  2:238757/1‑147 (MQ=255)                                                                                ttttCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCTGATTGGCg                                                                  >  4:335438/1‑147 (MQ=255)                                                                                  ttCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCTGATTGGCGAAg                                                               <  4:147982/148‑1 (MQ=255)                                                                                  ttCTCAGGAATGCACCGGTTTC‑GCACGCTCACGCAGAATTGTACGCAGGCATT‑CGCCGACGGAAGGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGTCAGCTCCTTGGTCTGATTGCCGCAg                                                               <  2:323264/148‑1 (MQ=255)                                                                                     tcAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCTTTGGTCTGATTGGCGAAGCAg                                                            >  1:162259/1‑148 (MQ=255)                                                                                       aGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCTGATTGGCGAAGCAGTAc                                                         >  4:321173/1‑149 (MQ=255)                                                                                            tGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGGATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCTGATTGGCGAAGCAGTACCAcgc                                                    >  5:360338/1‑149 (MQ=255)                                                                                               aCCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCTGATTGGc                                                                   <  2:44921/131‑1 (MQ=255)                                                                                               aCCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCTGATTGGc                                                                   >  1:44921/1‑131 (MQ=255)                                                                                                   gTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGACTCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCTGATTGGCGAAGCAGTACCACGCGGGTTtc                                             <  5:174129/149‑1 (MQ=255)                                                                                                           aaGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCTGATTGGCGAAGCAGTACCACGCGGGTTTCTCTTcga                                      <  3:82896/149‑1 (MQ=255)                                                                                                                cACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCTGATTGGCGAAGCAGTACCACGCGGGTTTCTCTTCGACGaa                                  <  4:358196/148‑1 (MQ=255)                                                                                                                            tACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCTGATTGGCGAAGCAGTACCACGCGGGTTTCTCTTCGACGAAGATCTGCAGGTc                      >  6:127035/1‑148 (MQ=255)                                                                                                                               ggAGGCATTCCGTCGGC‑GAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCTGATTGGCGAAGCAGTACCACGCGGGTTTCTCTTCGACGAAGATCTGCAGGTCGaa                   >  7:34391/1‑148 (MQ=255)                                                                                                                                     aTT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCTTTGGTCTGATTGGCGAAGCAGTACCACGCGGGTTTCTCTTCGACGAAGATCTGCAGGTCGAAATCCCAg            <  2:162259/149‑1 (MQ=255)                                                                                                                                            cGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCGTGGTCTGATTGGCGAAGCAGTACCACGCGGGTTTCTCTTAGACGAAGCTCTGCAGGTCGAAATCCCAggaatgg      >  2:334391/1‑144 (MQ=255)                                                                                                                                                ggAATGCCTCCGTACAGACATGACGTTGAATCAGCTTTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCTGATTGGCGAAGCAGTACCACGCGGGTTTCTCTTCGACGAAGATCTGCAGGTCGAAATCCCAGGCTTGGTCGc  >  4:263110/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                                     CGTCTCCCTCGACCAGGTCGATGATCTGCAGTTCTTGGCTCACG‑GGTACACTCCAAACGCTGAAAAACAAAACCGCCCTTTTCTCAGGAATGCACCGGTTTG‑GCAAGTTCACGCAGAATTGTACGGAGGCATT‑CGCCGACGGAATGCCTCCGTACAGACATGACGTTGAATCAGCTGTTCTGCTCGAACACCTCTTGGCCGGACAGCTCCTTGGTCTGATTGGCGAAGCAGTACCACGCGGGTTTCTCTTCGACGAAGATCTGCAGGTCGAAATCCCAGGCTTGGTCGC  >  NC_002947/4905364‑4905652

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: ‑