Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,234,799	T→C	10.8%	intergenic (+40/‑107)	PP_2833 → / → PP_2834	LysR family transcriptional regulator/D‑galactarate dehydratase/altronate dehydratase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,234,799	0	T	C	10.8%	115.9 / 4.8	46	intergenic (+40/‑107)	PP_2833/PP_2834	LysR family transcriptional regulator/D‑galactarate dehydratase/altronate dehydratase
Reads supporting (aligned to +/- strand):  ref base T (21/20);  new base C (2/3);  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 = 1.00e+00

CCGCAAGGATGAACCGCTCAGCGCCTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCTGAGAGGTCCCATGCAACTGATTGCCAAATCCGGTGACCCCGCCGTCAT  >  NC_002947/3234651‑3234943                                                                                                                                                     |                                                                                                                                                 ccGCAAGGATGAACCGCTCAGCGCCTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACt                                                                                                                                                  >  5:30691/1‑149 (MQ=255)   gCAAGGATGAACCGCTCAGCGCCTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACtt                                                                                                                                                 >  7:213724/1‑148 (MQ=255)   gCAAGGATGAACCGCTCAGCGCCTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTc                                                                                                                                                <  5:264478/149‑1 (MQ=255)    cAAGGATGAACCGCTCAGCGCCTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCa                                                                                                                                               <  7:208305/149‑1 (MQ=255)          tGAACCGCTCAGCGCCTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTAt                                                                                                                                         >  3:328479/1‑149 (MQ=255)             aCCGCTCAGCGCCTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGCCACTGCGTTCTGCCCCTAGCCGATTGAAGATAACGTTCCGAAATACGCGTTCGATAACTTCAGGTTATCGc                                                                                                                                      >  8:245489/1‑149 (MQ=255)             aCCGCTCAGCGCCTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACCTGAAGTTATCg                                                                                                                                       >  5:230207/1‑148 (MQ=255)              ccGCTCAGCGCCTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACCTGAAGTTATCga                                                                                                                                      >  4:251382/1‑147 (MQ=255)               cGCTCAGCGCCTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACCTGAAGTTATCgaaa                                                                                                                                    <  6:230207/149‑4 (MQ=255)                gCTCAGCGCCTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACCTGAAGTTATCgaaag                                                                                                                                   <  3:251382/149‑5 (MQ=255)                    aGCGCCTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATc                                                                                                                                <  6:30691/148‑1 (MQ=255)                        ccTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGatc                                                                                                                           <  2:149223/149‑1 (MQ=255)                         cTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCg                                                                                                                               >  6:22386/1‑144 (MQ=255)                         cTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCg                                                                                                                               <  5:22386/144‑1 (MQ=255)                                  ggCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCTGCTGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTgg                                                                                                                 <  8:123302/149‑1 (MQ=255)                                   gCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCAtctc                                                                                                                      <  6:352140/143‑1 (MQ=255)                                   gCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCAtctc                                                                                                                      >  5:352140/1‑143 (MQ=255)                                                     ctgGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGcttc                                                                                              <  6:210809/149‑1 (MQ=255)                                                      tgGAGCGCGCGCAACGCCGGCAGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCACATTGGGAATGAGGCACCAGGcatct                                                                                             >  4:222836/1‑149 (MQ=255)                                                          gggCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTa                                                                                           >  1:153194/1‑147 (MQ=255)                                                          gggCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGGTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCCCCAGGCTTCTTACa                                                                                         >  5:268240/1‑149 (MQ=255)                                                           ggCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAg                                                                                        >  4:41157/1‑149 (MQ=255)                                                                  aaCGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTAc                                                                                 <  5:112455/149‑1 (MQ=255)                                                                     gCCGGCGACAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGc                                                                              <  6:56837/149‑1 (MQ=255)                                                                          cggcAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGTAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATaa                                                                         <  3:222836/149‑1 (MQ=255)                                                                                tCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACaag                                                                     >  7:279885/1‑147 (MQ=255)                                                                                      gAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCCCCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGc                                                             <  6:268240/149‑1 (MQ=255)                                                                                            acTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTcc                                                       >  4:222301/1‑149 (MQ=255)                                                                                                cGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGc                                                     <  7:245489/147‑1 (MQ=255)                                                                                                 gTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTg                                                                                      >  5:79748/1‑113 (MQ=255)                                                                                                 gTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTg                                                                                      <  6:79748/113‑1 (MQ=255)                                                                                                       ccccTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATAGATCGATCGCATCATATCATTGGGAATGCGTCACCAGGCTTATTAAAGTGGCTACAGCCATAAAAAGAATTCATCCGCTCCGCCCTGagag                                             >  7:9166/1‑148 (MQ=255)                                                                                                        cccTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCTGAGAGGt                                           >  3:228588/1‑149 (MQ=255)                                                                                                                    gAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCTGAGAGGTCCCATGCAACt                                >  5:156943/1‑148 (MQ=255)                                                                                                                         tCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGACAGCCGATCCGCCCTGAGAGGTCCCATGCAACTGATTGc                          >  2:326923/1‑149 (MQ=255)                                                                                                                          cACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCAGAGAGGTCCCATGCAACTGATTGc                          >  1:150556/1‑148 (MQ=255)                                                                                                                           aCGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCTGAGAGGTCCCATGCAACTGATTGcc                         <  6:156943/148‑1 (MQ=255)                                                                                                                             gTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCTGAGAGGTCCCATGCAACTGATTGCCaaa                      <  2:153194/149‑1 (MQ=255)                                                                                                                                ccGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCTGAGAGGTCCCATGCAACTGATTGCCAAATc                    <  5:352855/148‑1 (MQ=255)                                                                                                                                  gAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCa                                                               <  6:77409/103‑1 (MQ=255)                                                                                                                                  gAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCa                                                               >  5:77409/1‑103 (MQ=255)                                                                                                                                   aaaTACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCTGAGAGGTc                                          >  8:189777/1‑123 (MQ=255)                                                                                                                                        atcgatCGATAACCTGAAGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCTGagag                                             <  5:235588/110‑1 (MQ=255)                                                                                                                                                aTAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCTga                                                >  6:4688/1‑104 (MQ=255)                                                                                                                                                aTAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCTga                                                <  5:4688/104‑1 (MQ=255)                                                                                                                                                aTAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCTGAGAGGTCCCATGCAACTGATTGCCAAATCCGGTGACCCCGCCGTCa   >  1:184928/1‑149 (MQ=255)                                                                                                                                                 tAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCTGAGAGGTCCCATGCAACTGATTGCCAAATCCGGTGACCCCGCCGTCAt  >  6:311124/1‑149 (MQ=255)                                                                                                                                                 tAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCTGAGAGGTCCCATGCAACTGATTGCCAAATCCGGTGACCCCGCCGTCAt  <  2:150556/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                 CCGCAAGGATGAACCGCTCAGCGCCTCCGCCAGGGCGTTTGTCGAGATTCTGCTGGAGGGCGCGCAACGCCGGCGGCAATCTTCGGAAGACACTGCGTTCTGCCCCTAGCCGATTGAAGATCACGTACCGAAATACCCTTTCGATAACTTCAGGTTATCGCTCGATCGGATCATCTCATTGGGAATGCGGCACCAGGCTTCTTACAGTGGCTACAGCCATAACAAGAAGTCAGCCGCTCCGCCCTGAGAGGTCCCATGCAACTGATTGCCAAATCCGGTGACCCCGCCGTCAT  >  NC_002947/3234651‑3234943

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: ‑