Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,132,149	G→A	G99D (GGC→GAC)	flgD →	flagellar biosynthesis, initiation of hook assembly

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,132,149	0	G	A	87.5%	33.6 / ‑4.8	17	G99D (GGC→GAC)	flgD	flagellar biosynthesis, initiation of hook assembly
Reads supporting (aligned to +/- strand):  ref base G (0/1);  major base A (9/5);  minor base T (1/1);  total (10/7)
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

GTTCGCTCACGGGCAGCAACGCCGCAGATTTACAAAGCAGTTTTCTGACTTTGCTGGTGGCGCAGCTGAAAAACCAGGACCCGACCAATCCAATGGAAAACAACGAGCTGACGTCGCAATTGGCACAAATCAGCACGGTCAGCGGGATTGAAAAACTCAATACCACGCTCGGATCTATTTCCGGACAGATTGATAACAGCCAGTCGTTACAGGCCAGTAACCTGATCGGTCACGGCGTGATGATCCCCGGCACCACTGTTCTTGCGGGAACCGGCAGTGAAGAAGGGGCTGTGACCACGACCACGCCGTTTGGTGTTGAGCTGCAACAGGCGGCAGACAAAGTTACGGCCACCATCACCGATAAAAATGGCGCGGTTGTGCGCACCATTGATATTGGTGAACTGACCGCCGGAGTTCACAGTTTCACCTGGGACGGTACGTTGACTGATGGCAGCACTGCGCCGAACGGT  >  NC_000913/1131915‑1132384                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                            gtTCGCTCACGGGCAGCAACGCCGCAGATTTACAAAGCAGTTTTCTGACTTTGCTGGTGGCGCAGCTGAAAAACCAGGACCCGACCAATCCAATGGAAAACAACGAGCTGACGTCGCAATTGGCACAAATCAGCACGGTCAGCGGGATTGAAAAACTCAATACCACGCTCGGATCTATTTCCGGACAGATTGATAACAGCCAGTCGTTACAGGCCAGTAACCTGATCGGTCACGACGTGATGATCCCCGGc                                                                                                                                                                                                                             >  1:68907/1‑251 (MQ=255)                      ccgcAGCTTTACAAAGCAGTTTTCTGACTTTGCTGGTGGCGCAGCTGAAAAACCAGGACCCGACCAATCCAATGGAAAACAACGAGCTGACGTCGCAATTGGCACACATCAGCACGGTCAGCGGGATTGAAAAACTCAATACCACGCTCGGATCTATTTCCGGACAGATTGATAACAGCCAGTCGTTACAGGCCAGTAACCTGATCGGTCACGACGTGATGATccc                                                                                                                                                                                                                                 >  1:116006/1‑226 (MQ=255)                                                                                              tGGAAAACAACGAGCTGACGTCGCAATTGGCACAAATCAGAACGGTCAGCGGGATTGAAAAACTCAATACCACGCTCGGATCTATTTCCGGACAGATTGATAACAGCCAGTCGTTACAGGCCAGTAACCTGATCGGTCACGACGTGATGATCCCCGGcac                                                                                                                                                                                                                           >  1:331625/1‑160 (MQ=255)                                                                                                                            cacaAATCAGCACGGTCAGAGGGGTTGAAGAACTCACTAACACGCTCGGTTCTATTTCCGGACAGATTGATAACCGCCAGTCGTTCCAGGCCCGTAACATGATCGGTCACGACGTGATGATCCCCGGCACCACTGTTCTTGCGGGAACCGCCAGTGAAGAAGGGGCTGTGACCCCGACCACGCCGTTTGGTGTTGAGCTGCAACAGGCGGCAGACAAAGTTAc                                                                                                                              >  1:429352/1‑223 (MQ=255)                                                                                                                              caactCAGCACGGTCATCGTGATTGAAAAACGCAAGACCTCGCTCGGATCTATTTCCGGACAGATTGATAACAGCCAGTCGTTACAGTCCAGTAAACTGATCGGTCACGACGTGATGATCCCCGGCACCACTGTTCTTGCGGGAACCGTCAGTGAATAAGGGGCTGTGACCACGACCGCTCCGGTTGGTGTTGAGCTGCAACAGGCGGCAGACAAAGTTACGGCCACGATCACCGATAAAAATGGCGCGGt                                                                                                <  1:194248/247‑1 (MQ=255)                                                                                                                                     gCACGGTCAGCGGTATTGAAAAACTCAATACCACGCTCGGATCTATTTCCGGACAGATTGATAACAGCCAGTCGTTACAGGCCAGTAACCTGATCGGTCACGACGTGATGATCCCCGGCGCCACTGTTCTTGCGTGATCCGGCAGTGAAGAAGGGGCTGTGTCCACGACCACGCCGTTTGGTGTTGAGCTGCAACAGGCGGCAGACAAAGTTACGGCCACCATCACCGATAAAAATGGCGCGGTTGTgcgc                                                                                         <  1:332307/251‑1 (MQ=255)                                                                                                                                            cAGCGGGATTGAAAAACTCAATACCACGCTCGGATCTATTTCCGGACAGATTGATAACAGCCAGTCGTTACAGGCCAGTAACCTGATCGGTCACGACGTGATGATCCCCGGCACCACTGTTCTTGCGGGAACCGGCAGTGAAGAAGGGGCTGTGACCACGACCACGCCGTTTGGTGTTGAGCTGCAACAGGCGGCAGACAAAGTTACGGCCACCATCACCGATAAAAATGGCGCGGTTGTGCGCACCATTg                                                                                  <  1:177306/251‑1 (MQ=255)                                                                                                                                                   aTTGAAAAACTCAATACCACGCTCGGATATATTTCCGGCCAGATTGATAACAGCCAGTCGTTACAGGCCAGTAACCTGCTCGGTCACGACGTGATGATCCCCGGCAACACTGTTCTTACGGGAACCGGCAGTGAAGAAGGGGCTGTGACCACGACCACGCCGTTTGGTGTTGAGCTGCAACAGGCGGCAGa                                                                                                                                       >  1:182233/1‑191 (MQ=255)                                                                                                                                                      naaaaaCTCAATACCACGCTCGGATCTATTTCCGGACAGATTGATAACAGCCAGTCGTTACAGGCCAGTAACCTGATCGGTCACGACGTGATGATCCCCGGCACCACTGTTCTTGCGGGAACCGGCAGTGAAGAAGGGGCTGTGACCACGACCACGCCGTTTGGTGTTGAGc                                                                                                                                                       >  1:149169/2‑172 (MQ=255)                                                                                                                                                            cTCAATACCACGCTCGGATCTATTTCCGGACAGATTGATAACAGCCAGTCGTAACAGGCCAGTCACCTGATCGGTCACGACGTGATGATCCCCGGCACCACTGTTCTTGCGGGAACCGGCAGTGAAGAAGGGGCTGTgaccacgac                                                                                                                                                                           >  1:293603/1‑146 (MQ=255)                                                                                                                                                                                                     cAGCCAGTCGTTACAGGCCAGTAACCTGATCGGTCCCGACGTGATGATCCCCGGCACCACTGTTCTTGCGGGAACCGGCAGTGAAGAAGGGGCTGTGACCACGACCACGCCGTTTGGTGTTGAGCTGCAACAGGCGGCAGACAAAGTTACGGCCACCATCACCGATAAAAATGGCGCGGTTGTGCGCACCATTGATATTGGTGAACTGACCGCCGGAGTTCACAGTTTCACCTGGGACGGTACGTTGACtn                         <  1:104626/251‑2 (MQ=255)                                                                                                                                                                                                              nttACAGGCCAGTAACCTGATCGGTCACGACGTGATGATCCCCGGCACCACTGTTCTTGCGGGAAACGGCAGTGAAGAAGGGGCTGTGACCACGACCACGCCGTTTGGTGTTGAGCTGCAACAGGCGGCAGACAAAGTTACGGCCACCATCACCGATAAAAATGGCGCGGTTGTGCGCACCATTGATATTGGTGAAATGCCCGCCGGCGTTCACAGTTTCACCTGGGACGGAACGTTGa                            >  1:60855/2‑239 (MQ=255)                                                                                                                                                                                                              gTTACAGGCCAGTAACCGGATCGGTCACGTCGTGATGATCCCCGGCACCACTGTTCTCGCGGGAACCGGCAGTGAAGAAGGTGCTGGGACCACGGCCACGCCGTTTGGTGTTGAGCTGCAACAGGCGGCAGACAAAGTTACGGCCACCATCACCGATa                                                                                                             <  1:281151/158‑1 (MQ=255)                                                                                                                                                                                                                  cAGGCNAGTAANCNNATCGGTCACGTCGTGATGANCCCCGGCACCACTGTNCTTGNGGGAANCGNcn                                                                                                                                                                                                    >  2:208635/1‑66 (MQ=255)                                                                                                                                                                                                                  cAGGCCAGTAACCTGATCGGTCACGACGTGATGATCCCCGGCACCACTGTTCTTGCGGGAACCGGCAGTGAAGAAGGGGCTGTGACCACGACCACGCCGTTTGGTGTTGAGCTGCAACAGGCGGCAGACAAAGTTACGGCCACCATCACCGATAAAAATGGCGCGGTTGTGCGCACCATTGATATTGGTGAACTGACCGCCGGAGTTCACAGTTTCACCTg                                          <  1:208635/221‑1 (MQ=255)                                                                                                                                                                                                                  cAGGCCAGTAACCTGATCGGGCACGGCGTGATGATCCCCGGCACCACTGGTCGTGCGGGAACCGGCAGTGAAGAAGGGGCTGTGACCACTACCACGCCGTTTGGTGTTGAGCGGCAACAGGCGGCAGACAAAGTTACGGCCACCATCACCGATAAAAATGGCGCGGt                                                                                                <  1:433936/167‑1 (MQ=255)                                                                                                                                                                                                                            aCCTGATCGGTCACGACGTGATGATCCCCGGCACCACTGATCTTGCGGGAACCGGCAGTGACGAAGGGGCTGTGACCACGACCACGCCGTTTGGTGTTGAGCTGCAACAGGCGGCAGACAAAGTTACGGCCACCATCACCGATAAAAATAGCGCGGTTGTGCGCACCATTGATATTGGTGAACTTACCGCCGGAATTCACAGTTTCACCTGGGACGGTACGTTGACTGATGGCAGCACTGCGCCGAACGGt  >  1:221136/1‑251 (MQ=255)                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                            GTTCGCTCACGGGCAGCAACGCCGCAGATTTACAAAGCAGTTTTCTGACTTTGCTGGTGGCGCAGCTGAAAAACCAGGACCCGACCAATCCAATGGAAAACAACGAGCTGACGTCGCAATTGGCACAAATCAGCACGGTCAGCGGGATTGAAAAACTCAATACCACGCTCGGATCTATTTCCGGACAGATTGATAACAGCCAGTCGTTACAGGCCAGTAACCTGATCGGTCACGGCGTGATGATCCCCGGCACCACTGTTCTTGCGGGAACCGGCAGTGAAGAAGGGGCTGTGACCACGACCACGCCGTTTGGTGTTGAGCTGCAACAGGCGGCAGACAAAGTTACGGCCACCATCACCGATAAAAATGGCGCGGTTGTGCGCACCATTGATATTGGTGAACTGACCGCCGGAGTTCACAGTTTCACCTGGGACGGTACGTTGACTGATGGCAGCACTGCGCCGAACGGT  >  NC_000913/1131915‑1132384

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑