Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,615,623	A→G	9.6%	intergenic (‑102/+29)	hldE ← / ← msbA	bifunctional heptose 7‑phosphate kinase/heptose 1‑phosphate adenylyltransferase/lipid A export ATP‑binding/permease MsbA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,615,623	0	A	G	9.6%	134.2 / 4.7	52	intergenic (‑102/+29)	hldE/msbA	bifunctional heptose 7‑phosphate kinase/heptose 1‑phosphate adenylyltransferase/lipid A export ATP‑binding/permease MsbA
Reads supporting (aligned to +/- strand):  ref base A (25/22);  new base G (3/2);  total (28/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

CACCAGTACCGGGGCTTGATCGAAACGCGGCATGGACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTCGACCAGGCGGCCCTGGTC  >  NC_002947/5615477‑5615768                                                                                                                                                    |                                                                                                                                                  caccaGTACCGGGGCTTGATCGAAACGCAGCATGGACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAgg                                                                                                                                                 <  3:21240/149‑1 (MQ=255)                        aaCGCGGCATGGACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGcccc                                                                                                                                    >  3:141206/1‑139 (MQ=255)                        aaCGCGGCATGGACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGcccc                                                                                                                                    <  4:141206/139‑1 (MQ=255)                        aaCGCGGCATGGACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAaggag                                                                                                                          <  1:69799/149‑1 (MQ=255)                        aaCGCGGCATGGACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAaggag                                                                                                                          >  2:41563/1‑149 (MQ=255)                             ggCATGGACATCTTCATTGGCAACCCATATTGAAATAATGAACAGGGGCAGTATTTTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCATCCCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGtt                                                                                                                      <  1:70144/149‑1 (MQ=255)                                  ggACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGt                                                                                                                 >  7:39773/1‑148 (MQ=255)                                   gACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCTCCGATCAAGGAGGGTTCAGGTg                                                                                                                <  8:39773/148‑1 (MQ=255)                                   gACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAagga                                                                                                                           >  1:227712/1‑137 (MQ=255)                                   gACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAagga                                                                                                                           <  2:227712/137‑1 (MQ=255)                                         ttCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCgg                                                                                                         >  6:32496/1‑149 (MQ=255)                                             tGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCtt                                                                                                     >  4:36127/1‑149 (MQ=255)                                             tGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGAAGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCtt                                                                                                     >  4:198055/1‑149 (MQ=255)                                                 cAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGcc                                                                                                 >  1:166915/1‑149 (MQ=255)                                                            gAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCa                                                                                       <  1:41563/148‑1 (MQ=255)                                                                         ggggCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATg                                                                          >  8:217640/1‑148 (MQ=255)                                                                            gCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGc                                                                                     <  1:855/134‑1 (MQ=255)                                                                            gCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGc                                                                                     >  2:855/1‑134 (MQ=255)                                                                                      aGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATaa                                                             <  5:32496/148‑1 (MQ=255)                                                                                       gCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATg                                                           >  1:125613/1‑149 (MQ=255)                                                                                        cacaGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATgg                                                          >  8:234606/1‑149 (MQ=255)                                                                                         acaGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAggg                                                                                                                        <  5:92013/86‑1 (MQ=255)                                                                                         acaGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAggg                                                                                                                        >  6:92013/1‑86 (MQ=255)                                                                                             ggTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCAt                                                      >  6:71856/1‑148 (MQ=255)                                                                                              gTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCa                                                                        >  3:16063/1‑129 (MQ=255)                                                                                              gTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCa                                                                        <  4:16063/129‑1 (MQ=255)                                                                                                 gTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGcc                                                 <  2:125613/149‑1 (MQ=255)                                                                                                  tCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAg                                                                                                                   <  7:155122/82‑1 (MQ=255)                                                                                                  tCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCg                                                >  1:74957/1‑149 (MQ=255)                                                                                                   cAATGGCTTTATGGCCAGATCAT‑CCCAGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTCATATCGGCCTTGGCAGGCTCATCCAGCCCCATCGCATGCAAACGCGCATAAAGGCCATTAGCCg                                                >  5:43165/1‑148 (MQ=255)                                                                                                            tATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAagcagc                                        <  7:217640/147‑1 (MQ=255)                                                                                                             aTGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATa                                                              <  4:115718/124‑1 (MQ=255)                                                                                                             aTGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATa                                                              >  3:115718/1‑124 (MQ=255)                                                                                                               ggCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGgt                                   >  5:67230/1‑149 (MQ=255)                                                                                                                 ccAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATgg                                                                              >  6:218498/1‑104 (MQ=255)                                                                                                                 ccAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATgg                                                                              <  5:218498/104‑1 (MQ=255)                                                                                                                 ccAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGgtgt                                 <  7:234606/149‑1 (MQ=255)                                                                                                                  cAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGtgtg                                <  6:67230/149‑1 (MQ=255)                                                                                                                              tGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCt                     >  6:87301/1‑149 (MQ=255)                                                                                                                                gAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTc                    >  1:155448/1‑148 (MQ=255)                                                                                                                                        ccGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGtgtg                                <  2:8370/128‑1 (MQ=255)                                                                                                                                        ccGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGtgtg                                >  1:8370/1‑128 (MQ=255)                                                                                                                                        ccGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTCGACCAggcg           <  6:158405/149‑1 (MQ=255)                                                                                                                                          tccttgaTCGGGGCCGTCATGGCCTCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTCGACCAggcggc         >  5:276286/7‑149 (MQ=255)                                                                                                                                            cttgaTCGGGGCCGTCATGGCCTCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTCGACCAggcggc         <  6:276286/143‑1 (MQ=255)                                                                                                                                             ttgaTCGGGGCCGTCATGGCCTCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTCGACCAggcgg          >  7:82668/4‑145 (MQ=255)                                                                                                                                             ttgaTCGGGGCCGTCATGGCCTCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTCGACCAggcgg          <  8:82668/142‑1 (MQ=255)                                                                                                                                             aCAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTCGACCAGGCGGCCCt      <  5:179382/149‑1 (MQ=255)                                                                                                                                               gaTCGGGGCCGTCATGGCCTCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTCGACCAGGCGGCCCTgg    >  6:1220/2‑149 (MQ=255)                                                                                                                                               aaTCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTCGACCAGGCGGCCCTgg    <  3:36127/149‑1 (MQ=255)                                                                                                                                               aaTCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCAAAACATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTCGACCAGGCGGCCCTgg    >  1:218523/1‑149 (MQ=255)                                                                                                                                                 tCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAATCGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTCGACCAGGCGGCCCTGGTc  >  3:142514/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                  CACCAGTACCGGGGCTTGATCGAAACGCGGCATGGACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTCGACCAGGCGGCCCTGGTC  >  NC_002947/5615477‑5615768

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑