Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC	NC_000913	3,822,651	(CAGGAT)1→2	coding (252/2109 nt)	spoT →	bifunctional (p)ppGpp synthase/hydrolase SpoT

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3822646 =	1 (0.050)	9 (0.470)	9/278	0.6	94.7%	coding (247/2109 nt)	spoT	bifunctional (p)ppGpp synthase/hydrolase SpoT
	?	NC_000913	= 3822651	0 (0.000)					coding (252/2109 nt)	spoT	bifunctional (p)ppGpp synthase/hydrolase SpoT

CTGATTCAAACCTACCTGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGTTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAACAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGATGGTGCAGGATATCCGCGTCATCCTCATCAAACTTGCCGACCGTACCCACAACATGCGCACGCTGGGCTCACTTCGCCCGGACAAACGTCGCCGCATCGCCCGTGAAACTCTCGAAATTTATAG  >  NC_000913/3822427‑3822899                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                         caaacctacctgccggaagaccaaatcaagcgtctgcggcaggcgtatctcgttgcacgtgatgctcacgaggggcaaacacgttcaagcggtgaaccctatatcacgcacccggtagcggttgcctgcattctggccgagatgaaactcgactatgaaacgctgatggcggcgctgctgcatgacgtgattgaagatactcccgccacctaccaggatCAGGATATGGAACAGCTTTTTGGTAAAAGCGt                                                                                                                                                                                                                                <  1:174458‑M1/32‑1 (MQ=255)       cAAACCTACCTGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGTTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATcaggatatggaacagctttttggtaaaagcgt                                                                                                                                                                                                                          <  1:174458‑M2/251‑33 (MQ=255)                           caagcgtctgctgcaggcgtatctcgttgcacgtgatgctcacgaggggcaaacacgttcaagcggtgaaccctatatcacgcacccggtagcggttgcctgcattctggccgagatgaaactcgactatgaaacgctgatggcggcgctgctgcatgacgtgattgaagatactcccgccacctaccaggatCAGGATATGGAACAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGAGTGTCg                                                                                                                                                                                                       >  1:11008‑M1/194‑250 (MQ=255)                                 cAAGCGTCTGCTGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGTTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATcaggatatggaacagctttttggtaaaagcgtcgccgagctggtagagggagtgtcg                                                                                                                                                                                                 >  1:11008‑M2/1‑193 (MQ=255)                                                      tgcacgtgatgctcacgaggggcaaacacgttcaagcggtcaaccctatatcacgcccccggtagaggttgcctgcattctggccgagctgaaactagactatgaaacgctgatggcggcgctgctgcatgccgtgattgaagatacttccgccacctaccaggatCAGGATATGGAACAGCTTTTTGGTAAAAGCGTCGCCGCGATGGTAGAgggg                                                                                                                                                                                                             <  1:502370‑M1/51‑1 (MQ=255)                                                            tGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTCAACCCTATATCACGCCCCCGGTAGAGGTTGCCTGCATTCTGGCCGAGCTGAAACTAGACTATGAAACGCTGATGGCGGCGCTGCTGCATGCCGTGATTGAAGATACTTCCGCCACCTACCAGGATcaggatatggaacagctttttggtaaaagcgtcgccgcgatggtagagggg                                                                                                                                                                                                       <  1:502370‑M2/217‑52 (MQ=255)                                                                                                               cccggtagcggttgcctgcattctggccgagatgaaactcgactatgacacgctgatggcggcgctgctgcctgacgtgattgaagctactcccgccacctaccaggatCAGGATATGGAACAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAagag                                                                                                                                                                   <  1:84505‑M1/93‑1 (MQ=255)                                                                                                                     cccGGTAGCGGTTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGACACGCTGATGGCGGCGCTGCTGCCTGACGTGATTGAAGCTACTCCCGCCACCTACCAGGATcaggatatggaacagctttttggtaaaagcgtcgccgagctggtagagggggtgtcgaaacttgataaactcaagttccgcgataagaaagag                                                                                                                                                             <  1:84505‑M2/202‑94 (MQ=255)                                                                                                                      gcggttgcctgcattctggcagagatgaaactagactatgcaacgctgctagcggcgctgctgcatgacgtgattgaagatactcccgccacctaccaggatCAGGATATGGAACAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAgg                                                                                                                                                            <  1:173713‑M1/100‑1 (MQ=255)                                                                                                                            gCGGTTGCCTGCATTCTGGCAGAGATGAAACTAGACTATGCAACGCTGCTAGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATcaggatatggaacagctttttggtaaaagcgtcgccgagctggtagagggggtgtcgaaacttgataaactcaagttccgcgataagaaagaggcgcagg                                                                                                                                                      <  1:173713‑M2/202‑101 (MQ=255)                                                                                                                                        gccgagatgaaactcgactatgaaacgctgatggcggcgctgctgcatgacgtgattgaagatactaccgccacctaccaggatCAGGATATGGAACAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGCGGGGGTGTCGCAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCa                                                                                                                                                              <  1:230333‑M1/98‑1 (MQ=255)                                                                                                                                         gcgagatgaaactcgactatgaaacgctgatggcggcgctgctgcatgacgtgagtgaagatactcccgccacctaccaggatCAGGATATGGAACAGCTTGTGGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGTTGTCGAAACTTGATAAACGCAAGGTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATGATGGCGATGGTGCAGGATATCCGCGGCATCCTCATCAAACTTGcc                                                                                        >  1:160578‑M1/84‑251 (MQ=255)                                                                                                                                              gCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTACCGCCACCTACCAGGATcaggatatggaacagctttttggtaaaagcgtcgccgagctggtagcgggggtgtcgcaacttgataaactcaagttccgcgataagaaagaggcgca                                                                                                                                                        <  1:230333‑M2/182‑99 (MQ=255)                                                                                                                                               gcgAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGAGTGAAGATACTCCCGCCACCTACCAGGATcaggatatggaacagcttgtgggtaaaagcgtcgccgagctggtagaggggttgtcgaaacttgataaacgcaaggtccgcgataagaaagaggcgcaggccgaaaactttcgcaagatgatgatggcgatggtgcaggatatccgcggcatcctcatcaaacttgcc                                                                                  >  1:160578‑M2/2‑83 (MQ=255)                                                                                                                                                                                  ctgcatgacgtgattgaagatcctaccgccacctaccaggatCAGGATATGGAACAGCTTTTTGGTAAAAGAGTCGACGAGCTGGTAGAggggg                                                                                                                                                                                                            <  1:409070‑M1/52‑1 (MQ=255)                                                                                                                                                                                        ctgcATGACGTGATTGAAGATCCTACCGCCACCTACCAGGATcaggatatggaacagctttttggtaaaagagtcgacgagctggtagaggggg                                                                                                                                                                                                      <  1:409070‑M2/94‑53 (MQ=255)                                                                                                                                                                                                                         gatCAGGATATGGAACAGCTTTTTGGTAATAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGCAACTTGATAAACTCACGTTCCGCGATAAGAACGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGATGGTGCAGGATATCCGCGTCATCCTCATCAACCTTGCCGACCGTACCCACAACATGCGCACGATGGGCTCACTTCGCCCGGACAAACGTCGCCGCATCGCCCGTGAAACTATcgaact        <  1:411768‑M1/248‑3 (MQ=255)                                                                                                                                                                                                                               gatcaggatatggaacagctttttggtaatagcgtcgccgagctggtagagggggtgtcgcaacttgataaactcacgttccgcgataagaacgaggcgcaggccgaaaactttcgcaagatgattatggcgatggtgcaggatatccgcgtcatcctcatcaaccttgccgaccgtacccacaacatgcgcacgatgggctcacttcgcccggacaaacgtcgccgcatcgcccgtgaaactatcgaact  <  1:411768‑M2/251‑249 (MQ=255)                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                         CTGATTCAAACCTACCTGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGTTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAACAGCTTTTTGGTAAAAGCGTCGCCGAGCTGGTAGAGGGGGTGTCGAAACTTGATAAACTCAAGTTCCGCGATAAGAAAGAGGCGCAGGCCGAAAACTTTCGCAAGATGATTATGGCGATGGTGCAGGATATCCGCGTCATCCTCATCAAACTTGCCGACCGTACCCACAACATGCGCACGCTGGGCTCACTTCGCCCGGACAAACGTCGCCGCATCGCCCGTGAAACTCTCGAAATTTATAG  >  NC_000913/3822427‑3822899

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: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.