Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,615,628	A→G	9.8%	intergenic (‑107/+24)	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	5,615,628	0	A	G	9.8%	134.3 / 5.1	51	intergenic (‑107/+24)	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 (25/21);  new base G (3/2);  total (28/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.99e-01

AACGCGGCATGGACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTCGACCAGGCGGCCCTGGTC  >  NC_002947/5615500‑5615768                                                                                                                                  |                                                                                                                                             aaCGCGGCATGGACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGcccc                                                                                                                                    <  4:141206/139‑1 (MQ=255) aaCGCGGCATGGACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGcccc                                                                                                                                    >  3:141206/1‑139 (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                                                                                                                        >  6:92013/1‑86 (MQ=255)                                                                  acaGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAggg                                                                                                                        <  5:92013/86‑1 (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                                                                              <  5:218498/104‑1 (MQ=255)                                                                                          ccAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATgg                                                                              >  6:218498/1‑104 (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)                                                                                                                                  |                                                                                                                                             AACGCGGCATGGACAACTTCATGGGCAACCCATATGGAAATAATGAACAGGGGCAGGATATTAGCACAGGGTAGTCAATGGCTTTATGGCCAGATCAT‑CCCTGGAAAATTCCCGTGACAATCGAGGCCATGACGGCCCCGATCAAGGAGGGTTCAGGTGATATCGGCCTTGGCCGGCTCATCCAGCCCCATGGCATGCAAACGGGCATAATGGCCATTAGCCGCAAGCAGCTCGGTGTGAGTACCGCGCTCGACCAGGCGGCCCTGGTC  >  NC_002947/5615500‑5615768

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: ‑