Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,041,211:1	+T	9.3%	intergenic (+189/‑473)	PP_5680 → / → PP_4447	Cro/CI family transcriptional regulator/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,041,211	1	.	T	9.3%	158.3 / 10.9	43	intergenic (+189/‑473)	PP_5680/PP_4447	Cro/CI family transcriptional regulator/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (20/19);  new base T (2/2);  total (22/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.77e-01

CCAGTCTCACATCTGACCCTGTCAGCGACGCTAATGACGGTGTTGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTAT  >  NC_002947/5041065‑5041351                                                                                                                                                    |                                                                                                                                             ccAGTCTCACAACAGACACTCTCAGCGACGCTAATGACGGTGTTGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCga‑g                                                                                                                                             >  6:200425/1‑148 (MQ=255)    gTCTCACATCTGACCCTGTCAGCGACGCTAATGACGGTGTTGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTC‑TCGGCGGGCTTAAGGCGCGCCGATgaaga                                                                                                                                         <  7:246301/149‑1 (MQ=38)     tctcACATCTGACCCTGTCAGCGACGCTAATGACGGTGTTGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAagag                                                                                                                                        >  3:114200/1‑149 (MQ=255)         acaTCTGACCCTGTCAGCGACGCTAATGACGGTGTTGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGcc                                                                                                                                      <  8:247376/147‑1 (MQ=255)            tCTGACCCTGTCAGCGACGCTAATGACGGTGTTGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAgaga                                                                                                                                 >  8:198080/1‑149 (MQ=255)             atctcccTGTCAGCGACGCTAATGACGGTGTTGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGAc                                                                                                                                <  7:189380/145‑1 (MQ=255)                aCCCTGTCAGCGACGCTAATGACGGTGTTGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGAcccc                                                                                                                             >  2:67629/1‑149 (MQ=255)                  ccTGTCAGCGACGCTAATGACGGTGTTGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGAc                                                                                                                                >  8:189380/1‑144 (MQ=255)                        aGCGACGCTAATGACGGTGTTGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGa                                                                                                                     >  6:73992/1‑149 (MQ=255)                                           ttGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGc                                                                                                  <  7:198080/149‑1 (MQ=255)                                              aTCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGt                                                                                               <  7:122539/149‑1 (MQ=255)                                                 cacaGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCATAAGGCGGttag                                                                                            <  2:214029/149‑3 (MQ=255)                                                     gagGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTg                                                                                        <  4:114200/149‑1 (MQ=255)                                                     gagGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTg                                                                                        <  5:113240/149‑1 (MQ=255)                                                      agGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGc                                                                                       <  4:114306/149‑1 (MQ=255)                                                                   gCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTctgct                                                                          <  5:73992/149‑1 (MQ=255)                                                                           gCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTAATAGGCTCGCCTTAAGCCAGCAGA‑GAATAGACAGAGACCCCGAGCAAGACCCCTAAACGCCTTATCGCGGTTTCTCTGCATCCCAGTCTGCTGCGAAGGc                                                                  >  3:293826/1‑149 (MQ=255)                                                                            cgcaaTTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGcc                                                                 <  3:233305/146‑1 (MQ=255)                                                                               aaTTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGTCGa                                                               >  8:232466/1‑148 (MQ=255)                                                                                        aTACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCGCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGt                                                      <  4:293826/148‑1 (MQ=255)                                                                                                  ctctGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTc                                           >  4:168748/1‑149 (MQ=255)                                                                                                   tctGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAAGCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAg                                                            <  1:127462/131‑1 (MQ=255)                                                                                                       cGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCTTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTa                                         <  1:67629/146‑1 (MQ=255)                                                                                                        gATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTAtt                                       <  3:286608/147‑1 (MQ=255)                                                                                                        gATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTAtt                                       >  4:286608/1‑147 (MQ=255)                                                                                                         aTGAGGACATGTCCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCGTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTAttttt                                    <  5:200425/149‑1 (MQ=255)                                                                                                                cATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTg                             >  1:213859/1‑149 (MQ=255)                                                                                                                 aTGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGTCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTgg                            <  7:232466/149‑1 (MQ=255)                                                                                                                   gACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGcc                          >  1:13205/1‑149 (MQ=255)                                                                                                                      ctctTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGa                                                        <  6:107647/116‑1 (MQ=255)                                                                                                                      ctctTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGa                                                        >  5:107647/1‑116 (MQ=255)                                                                                                                       tctTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTgcc                      >  8:164392/1‑147 (MQ=255)                                                                                                                          ttctCGGCGGGCTTAAGGCGCGCCGATGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCg                    >  2:156996/4‑149 (MQ=255)                                                                                                                           tctCGGCGGGCTTAAGGCGCGCCGATGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGCCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCg                    >  7:211061/3‑148 (MQ=255)                                                                                                                            ctCGGCGGGCTTAAGGCGCGCCGATGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGCCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCa                  <  8:211061/148‑1 (MQ=255)                                                                                                                            aTCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAg                 <  3:168748/149‑1 (MQ=255)                                                                                                                            aTCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAg                 >  3:62561/1‑149 (MQ=255)                                                                                                                                gcgcgcCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGc                           <  8:193525/135‑1 (MQ=255)                                                                                                                                gcgcgcCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGc                           >  7:193525/1‑135 (MQ=255)                                                                                                                                     ccTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCgtg        >  7:63405/1‑149 (MQ=255)                                                                                                                                      cTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCgtgt       >  2:260688/1‑149 (MQ=255)                                                                                                                                      cTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCgtgt       >  3:223787/1‑149 (MQ=255)                                                                                                                                           gCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTAt  >  6:174841/1‑149 (MQ=255)                                                                                                                                           gCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATGTTTCGACCTGGCCTGACCGCAGTAGCGCGTGTGCTAt  >  6:179382/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                             CCAGTCTCACATCTGACCCTGTCAGCGACGCTAATGACGGTGTTGATCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGA‑GAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGAGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTAT  >  NC_002947/5041065‑5041351

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: ‑