Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,269,702	C→T	intergenic (+313/+1)	rdlA → / ← ldrB	putative antisense regulatory RNA RdlA/small toxic polypeptide LdrB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,269,702	0	C	T	90.9%	54.6 / ‑4.6	23	intergenic (+313/+1)	rdlA/ldrB	putative antisense regulatory RNA RdlA/small toxic polypeptide LdrB
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base T (10/10);  total (11/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01

TGGATACTACGACTCAATTCATCTTCACTTCATCCCTGAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACCTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGCCAGGATCGGTGCCGCCAGGTCGTGCCAGAAAGTCATGGCAAACTGCGCGAGCGTCATATAGCCGCCTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTGTCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTGCGGGGGTTTTCTCTTTCCAGCAACCAATGCCACCAG  >  NC_000913/1269463‑1269947                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                        tgGATACTACGACTCAATTCATCTTCACTTCATCCCTGAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACTTT‑ACTTCCgg                                                                                                                                                                                                                                              <  2:92039/250‑1 (MQ=255)                   tCATCTTCACTTCATCCCTGAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACa                                                                                                                                                                                                                           >  2:27544/1‑250 (MQ=255)                   tCATCTTCACTTCATCCCTGAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACa                                                                                                                                                                                                                           <  1:27544/250‑1 (MQ=255)                         tcacttcaTCCCTGAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTg                                                                                                                                                                                                                    >  1:320338/1‑251 (MQ=255)                                    cTGAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAAtt                                                                                                                                                                                                         >  1:259619/1‑251 (MQ=255)                                         aTGTTTGCAATTAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCTAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGc                                                                                                                                                                                                    <  1:20114/251‑1 (MQ=255)                                           gTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTACCCCTTCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCCGACTGACGCCCGCTTT‑ACCTTTACTTCCGGTTACGCCACACA‑CCGCCAATCGCTGCGGTAATATTTCCCGcc                                                                                                                                                                                                   >  2:9006/1‑250 (MQ=14)                                                          tGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCGTGACGCCCGGCTTCAGTCT‑AATTCCGAGTAAGCGTC‑CAGCAGACAATAGCTGCGGTAATAATTGCCGCCAGGATCGGTgccgcc                                                                                                                                                                                    >  1:49899/1‑250 (MQ=14)                                                                         cAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGACAGCCAGACGCCCGGTTTCACTTC‑ACTTCCGGTTACGCCAC‑CAGCCATCACTCGCTCCGGTAGTAATTCCCGCCAGGAACGGAGCCGACAGGTCGTGCCCGaa                                                                                                                                                                      >  1:6996/1‑249 (MQ=14)                                                                                  ttACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAACGACAAAAATGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGCCAGGATCGGTGCCGCCAGGTCGTGCCAGAAAGTCATggaa                                                                                                                                                            >  1:12821/1‑248 (MQ=255)                                                                                               aTGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAAGGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGCCAGGATCg                                                                                                                                                                                            <  1:257299/205‑1 (MQ=25)                                                                                               aTGAGTGCTATGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTAACCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGCCAGGATCg                                                                                                                                                                                            >  2:257299/1‑205 (MQ=255)                                                                                                           gATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGCCAGGATCGGTGCCGCCAGGTCGTGCCAGAAAGTCATGGCAAACTGCGCGAGCGTCATATAgccgcc                                                                                                                                  >  1:86289/1‑251 (MQ=38)                                                                                                                 gCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGAAAAAAATGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGCCAGGATCGGTGCCGCCAGGTCGTGCCAGAAAGTCATGGCAAACTGCGCGAGCGTCATATAGCCGCCttgttg                                                                                                                            <  1:264942/251‑1 (MQ=37)                                                                                                                      cagttCGGGTTTCCAATTTTTACTTGTGTAAGGTATAAAGACAAAAATGGCCGCGGGCTGTTCCCCCGGCGGCCGGTTT‑CGGGCCCATATTGACATCGCTGCCGCCTTTCGCCCGTTTTCCCGTT‑ACTCCGGGTTACGCCCC‑TCGCAGACAATCGCTGCGGTAATAATTCCCGCCAGGATCGGTGCCGCCAGGTCGTGCCAGAAAGTCATGGCAAACTGCGCGAGCGTCATATAGCCGCCTTGTTGTAATg                                                                                                                       <  1:40603/247‑1 (MQ=11)                                                                                                                      cAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTACCCCGGCGGCCGGTTC‑CGGGCCCATATTGCCACCCCGGCAGCCGGACGCCCGTTTTCCCCTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGCCAGGATCGGTGCCGCCAGGTCGTGCCAGAAAGTCATGGCAAACTGCGCGAGCGTCATATAGCCGCCTTGTTGTAATg                                                                                                                       <  1:114615/251‑1 (MQ=11)                                                                                                                                       atTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGCCAGGATCGGTGCCGCCAGGTCGTGCCAGAAAGTCATGGCAAACTGCGCGAGCGTCATATAGCCGCCTTGTTGTAATGACAACATTTTGCGGCTa                                                                                                      <  1:342138/251‑1 (MQ=37)                                                                                                                                                                      ggccgcgtggtggtcccccTGCGGC‑GGTTTGCGGGCCAATATTGCCATCCCGGCAGCCGGCCGCCCGTTTTCATTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGCCAGGATCGGTGCCGCCAGGTCGTGCCAGAAAGTCATGGCAAACTGCGCGAGCGTCATATAGCCGCCTTGTTGTAATGACAACATGTTGCGGCTATTCTTGAAGTGTCTGGTTTCAAGATTAGccc                                                                       <  2:86289/236‑1 (MQ=11)                                                                                                                                                                               gtGTTCCCCCTGCGGCCGTTGT‑CGGGCGCCTATTGCCATCACGGCAGCCTGACGCCCGTTTTCACTTT‑ACTTCCGGTTACGCCCC‑CGGCCGACAATCGCGGCGGTAATAATTCCCGCCAGGATCGGTGCCGCCAGGTCGTGCCAGAAAGTCATGGCAAACTGCGCGAGCGTCATATAGCCGCCTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTGTCTGGTTTCAAGATTAGCCCCCGTTCtgt                                                              <  2:259619/250‑1 (MQ=11)                                                                                                                                                                                                   tt‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGCCAGGATCGGTGCCGCCAGGTCGTGCCAGAAAGTCATGGCAAACTGCGCGAGCGTCATATAGCCGCCTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTGTCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCa                                           <  1:9006/250‑1 (MQ=37)                                                                                                                                                                                                                                      cccGTTTTCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGCCAGGATCGGTGCCGCCAGGTCGTGCCAGAAAGTCATGGCAAACTGCGCGAGCGTCATATAGCCGCCTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTGTCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTGCGGGGGTTTTCTCTTTCCAg                  >  1:507385/1‑241 (MQ=37)                                                                                                                                                                                                                                         gTTTTCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGCCAGGATCGGTGCCGCCAGGTCGTGCCAGAAAGTCATGGCAAACTGCGCGAGCGTCATATAGCCGCCTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTGTCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTGCGGGGGTTTTCTCTTTCCAGCAACCAATGccac     >  2:236448/1‑251 (MQ=37)                                                                                                                                                                                                                                             tCACTTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGCCAGGATCGGTGCCGCCAGGTCGTGCCAGAAAGTCATGGCAAACTGCGCGAGCGTCATATAGCCGCCTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTGTCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTGCGGGGGTTTTCTCTTTCCAGCAACCAATGCCACCAg  <  1:236448/250‑1 (MQ=37)                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                        TGGATACTACGACTCAATTCATCTTCACTTCATCCCTGAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATAAAGACAAAAATGGCCGCAGGCTGTTACCCCTGCGGCCGGTTT‑CGGGCGCATATTGCCATCACGGCAGCCTGACGCCCGTTTTCACCTT‑ACTTCCGGTTACGCCAC‑CAGCCGACAATCGCTGCGGTAATAATTCCCGCCAGGATCGGTGCCGCCAGGTCGTGCCAGAAAGTCATGGCAAACTGCGCGAGCGTCATATAGCCGCCTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTGTCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTGCGGGGGTTTTCTCTTTCCAGCAACCAATGCCACCAG  >  NC_000913/1269463‑1269947

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑