Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,623,578	C→T	S180S (TCG→TCA)	lplA ←	lipoate‑‑protein ligase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,623,578	0	C	T	88.9%	58.9 / 0.7	27	S180S (TCG→TCA)	lplA	lipoate‑‑protein ligase A
Reads supporting (aligned to +/- strand):  ref base C (3/0);  new base T (17/7);  total (20/7)
Fisher's exact test for biased strand distribution p-value = 5.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.96e-01

GTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGCGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAATGGGCGAAAAAGGCCTCGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAACAGCTCGGTGAGGTTGGTCACGCGGGAACGTACCGACGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGAGTAGCAAGGTGCCGTGGTGGAAGCCGCGATCTTTGGTTTCGCGATAGGCCGAGCCTGAGACTTTGCGGTCGCCTTCGACGGTTTTCACCACCAGATCGTTACGTCCGGACGCTTCGGCGCTGACGCCGAGCGCGTTCAGCGCATTGAGCACAATCGACGTGGAGATAGTTTT  >  NC_000913/4623336‑4623826                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                          ctAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGACGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTCCGGGGAGATGATTTCCGCTTCTACACGCTCGCCATAATGGGCGAAAAAGGCCTTGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACGCGGGAACGCACTGAGGT‑AAt                                                                                                                                                                                                                                                  >  1:205750/2‑251 (MQ=255)     aGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGACGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTCCGGGGAGATGATTTCCGCTTCTACACGCTCGCCATAATGGGCGAAAAAGGCCTTGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACGCGGGAACGCACTGAGGT‑AATGCCt                                                                                                                                                                                                                                              >  1:163005/1‑251 (MQ=255)                 gtaggtGCGAGAATGCAGGAGCCTGGCCGAGGTTCCAGTCCCAGATACTCTGACGGGAAAAGGTTGCGGGGAAGTGGGGCAAGTCTGGCGTTTTGTCCGGGAAGATGATTTCCGTGTCAACACGCTCTCCATAATGGGCGAAAAAGGCCTGGGTTAGGGCCTCGCAACCCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGt                                                                                                                                                                                                                                  <  2:193712/246‑1 (MQ=255)                   agATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGACGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTCCGGGGAGATGATTTCCGCTTCTACACGCTCGCCATAATGGGCGAAAAAGGCCTTGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGttt                                                                                                                                                                                                                                >  1:150795/1‑251 (MQ=255)                    gATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGACGGGCCAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTCCGGGGAGATGATTTCCGCTTCTACACGCTCGCCATAATGGGCGAAAAAGGCCTTGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGATCGGGGAGGTTGGTACCGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCCGTTTc                                                                                                                                                                                                                               >  1:32411/1‑251 (MQ=255)                                                       tCCCAGCTACTCTGACGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTCCGGGGAGATGATTTCCGCTTCTACACGCTCGCCATAATGGGCGAAAAAGGCCTTGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCt                                                                                                                                                                                            >  1:369636/1‑251 (MQ=255)                                                        cccAGCTACTCTGACGGGCAAAGGTTTCGGAGAAATTTGGCAAGTCTGGCGTTTTGTCCGGGGAGATGATTTCCGCTTCTACACGCTCGCCATCATGGGCGAAAAAGGCCTTGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACGCGGGAACGCACTGAGGT‑CAGGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCCGGCGGCt                                                                                                                                                                                            >  1:99268/1‑250 (MQ=255)                                                         tcagccaatctGACGGGCAAAGGTATCGGCGAAGTTTGGCAAGCCTGGCGATTTGTCCGGGGAGATGATTTGCGCTTCTACACGCTCGCCATAATGGGCGAAGAAGGCATTGGGTATGGCCTCGCAAACCTGCTCATGGGTGATCACCGGCAGCAGTTCGGTGAGGTTGGTCACGCGTGAACGCACTG‑CGTTAATGCCTTTCGGCGCCAGTTTCTTTTTATCCGGATTGAGTTAGTTTGCAAggcggcga                                                                                                                                                                                           >  2:77052/9‑248 (MQ=255)                                                                                   cGGCGAAGTTTGGCAAGTCTGGCGTTTTGTCCGGGGAGATGATTTCCGCTTCTACACGCTCGCCATAATGGGCGAAAAAGGCCTTGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAGGTGCCg                                                                                                                                                                >  1:94662/1‑251 (MQ=255)                                                                                     gCGAAGTTTGGCAAGTCTGGCGTTTTGTCCGGGGAGATGATTTCCGCTTCTACACGCTCGCCATAATGGGCGAAAAAGGCCTTGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTCAGGTCGGCATTGAGCAGCAAGGTGCCgtg                                                                                                                                                              >  1:55998/1‑251 (MQ=255)                                                                                              ggCAAGTCTGGCGTTTTGTCCGGGGAGATGATTTCCGCTTCTACACGCTCGCCATAATGGGCGAAAAAGGCCTTGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCtttt                                                                                                                                                                                                                           <  1:200972/181‑1 (MQ=255)                                                                                                      tGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACACGCTCGCCATAATGGGCGAAAAAGGCCTCGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAACAGCTCGGTGAGGTTGGTCACGCGGGAACGTACCGACGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGAGTAGCAAGGTGCCGTGGTGGAAGCCGCGATCtt                                                                                                                                             >  1:188561/1‑251 (MQ=255)                                                                                                                              ttCCGCTTCTCCCCGCTCGCCATAAGGGGCGAAAAAGGCCTGGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGGGAGGTTGGTCACGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGACAGGCGGCTAAGGTCGGCATTGAGCAGCAAGGTGCCGTGGTGGAAGCCACGATCTTTGGTTTCGCGATAGGcctatcct                                                                                                                      <  2:130535/250‑7 (MQ=255)                                                                                                                                     tctacacgcTCGCCATAATGGGCGAAAAAGGCCTTGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAGGTGCCGTGGTGGAAGCCACGATCttt                                                                                                                                            >  1:313807/7‑221 (MQ=255)                                                                                                                                     tctacacgcTCGCCATAAGGGGCGAAAAAGGCCTTGGTTATGGCCGCGCAAACCTGCTCATGTGTGATCCCCGGCAGCAGCTCGGTTAGGTTGGTCACGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAGGTGCCGTGGTGGAAGCCACGATCttt                                                                                                                                            <  2:313807/215‑1 (MQ=255)                                                                                                                                            gcTCGCCATAATGGGCGAAAAAGGCCTTGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAGGTGCCGTGGTGGAAGCCACGATCTTTGGTTTCGCGATAGGCCGATCCTGAGACTTTGCGGTCg                                                                                                       >  1:348907/1‑251 (MQ=255)                                                                                                                                                       ggggCGAAAAAGGCCTTGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGGTGGTCACGCGGGAACGCACTGATGT‑AATGCCTTGCGCCGCCAGTTGCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTAAGGTCGGCATTTAGCAGCAAGGTGCCGTGGTGGAATCCACGATCTTTGGTTTCGCGATAGGCCGATCCTGAGACTTTGCGGTCGCCTTCGGCGGt                                                                                            <  1:36970/250‑1 (MQ=255)                                                                                                                                                              aaaaGGCCTTGGTTATGGCCACGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCCCGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGAAAGGTTGCCAGGCGCCTAGGGTCGGCATTGAGCAGCAAGGTGCCGTGGTGGGAGCCCCGATCTTTGGATTCGCGATAGGCCGCTCCTGAGACTTAGCGTTCGCCTTCGGCGGgttttatc                                                                                     >  2:128382/1‑247 (MQ=255)                                                                                                                                                                   gCCTTGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAGGTGCCGTGGTGGAAGCCACGATCTTTGGTTTCGCGATAGGCCGATCCTGAGACTTTGCGGTCGCCTTCGGCGGTTTTGaccacc                                                                                  >  1:201457/1‑249 (MQ=255)                                                                                                                                                                                    gCAAACCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACTCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAGGTGCCGTGGTGGAAGCCACGATCTTTGGTTTCGCGATAGGCCGATCCTGAGACTTTGCGGTCGCCTTCGGCGGTTTTTACCCCCCGATCGTTACGCCCGGa                                                                 >  1:124009/1‑249 (MQ=255)                                                                                                                                                                                      aaaCCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAACAAGGTGCCGTGGTGGAAGCCACGATCTTTGGTTTCGCGATAGGCCGATCCTGAGCCTTTGCGGTCGCCTTCGGCGGTTTTCCCCACCAGATCGTATCGTCCGGCCGcc                                                             >  2:9489/1‑250 (MQ=255)                                                                                                                                                                                       aaCCTGCTCATGGGTGATCCCCGGCAGCAGCTCGGTGAGGTTGGTCACGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAGGTGCCGTGGTGGAAGCCACGATCTTTGGTTTCGCGATAGGCCGATCCTGAGACTTTGCGGTCGCCTTCGGCGGTTTTCACCACACGATCGTTACGCCCGGACGCtt                                                            >  1:5892/1‑251 (MQ=255)                                                                                                                                                                                               cATGGGTGATCCCCGGCAGCAGATCGGAGAGGTTGGTCACGCGGGAACGCACTGAGGT‑ACTGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAGGTGACGTGGTGGAAGCCACGATCTTTGGTTTCGCGATAGGCCGATCCTGAGACTTTGCGGTCGCCTTCGGCGGTTTTTCCCACCAGATCGTTGCGCCCGGACGCTTCCGCGCTg                                                    >  2:191468/1‑251 (MQ=255)                                                                                                                                                                                               cATGGGTGATCCCCGGCAACAGCTCGGTGAGGTTGGTCACGCGGGAACGTACCGACGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGAGTAGCAAGGTGCTGTGGTGGAAGCCGCGATCTTTGGTTTCGCGATAGGCCGAGCCTGAGACTTTGCGGTCGCCTTCGACGGTTTTCACCACCAGATCGTTACGTCCGGACGCTTCGGCGCTg                                                    >  1:72714/1‑251 (MQ=255)                                                                                                                                                                                                           ccGGCAGCAGCTCTGTGAGGTTGGTCACGCGTGCACGGACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGAGATGTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAGGTGCCGTGGTGGACGCCACGATCTTTGGTTTCGCGATAGGCCGATCCTGAGACGTTGCGGTCGCCTTCGGCGGTTGTCACCACCAGATCGTTACGCCCGGACGCTTCGGCGTTGACGCCAAGcgcg                                        <  2:205750/251‑1 (MQ=255)                                                                                                                                                                                                                                    cACGCGGGAACGCACTGAGGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAGGTGCCGTGGTGGAAGCCACGATCTTTGGTTTCGCGATAGGCCGATCCTGAGACTTTGCGGTCGCCTTCGGCGGTTTTCACCACCAGATCGTTACGCCCGGACGCTTCGGCGCTGACGCCAAGCGCGTTCAGCGCATTGAGCACAATCGACg               <  1:363643/251‑1 (MQ=255)                                                                                                                                                                                                                                                 aCCGACGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGAGTAGCAAGGTGCCGTGGTGGAAGCCGCGATCTTTGGTTTCGCGATAGGCCGAGCCTGAGACTTTGCGGACGCCTTCGACGGTTTTCACCACCAGCTCGTTACGTCAGGACGCTTCGGCGCTGACGCCGAGCGCGTTCAGCGCATTTAGCCAAATCGACGAGGAGATAGtttt  >  2:162065/1‑251 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                          GTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGCGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAATGGGCGAAAAAGGCCTCGGTTATGGCCTCGCAAACCTGCTCATGGGTGATCCCCGGCAACAGCTCGGTGAGGTTGGTCACGCGGGAACGTACCGACGT‑AATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGAGTAGCAAGGTGCCGTGGTGGAAGCCGCGATCTTTGGTTTCGCGATAGGCCGAGCCTGAGACTTTGCGGTCGCCTTCGACGGTTTTCACCACCAGATCGTTACGTCCGGACGCTTCGGCGCTGACGCCGAGCGCGTTCAGCGCATTGAGCACAATCGACGTGGAGATAGTTTT  >  NC_000913/4623336‑4623826

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑