Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC JC	NC_000913	2,867,842	IS1 (–) +9 bp	31.2%	coding (904‑912/1140 nt)	nlpD ←	murein hydrolase activator NlpD

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2867842 =	85 (0.790)	41 (0.340)	34/176	NT	30.2%	coding (912/1140 nt)	nlpD	murein hydrolase activator NlpD
	?	NC_000913	3583428 =	NA (NA)					noncoding (1/768 nt)	IS1	repeat region
*	?	NC_000913	= 2867850	85 (0.790)	36 (0.300)	31/176	NT	27.5%	coding (904/1140 nt)	nlpD	murein hydrolase activator NlpD
	?	NC_000913	= 3584195	NA (NA)					noncoding (768/768 nt)	IS1	repeat region

TGGCGCTTCTGAGGGGGGCAACAAGGGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2867938‑2867842 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACT  >  NC_000913/3583428‑3583524                                                                                                                                                                                                    TGGCGCTTCTGAGGGGGGCAACAAGGGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGG                                                                                                 <  1:1986195/99‑1   GCGCTTCTGAGGGGGGCAACAAGGGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTG                                                                                               >  2:2462642/1‑99   GCGCTTCTGAGGGGGGCAACAAGGGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTG                                                                                               <  1:1253174/99‑1    CGCTTCTGAGGGGGGCAACAAGGGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGA                                                                                              <  1:750924/99‑1      CTTCTGAGGGGGGCAACAAGGGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATG                                                                                            <  2:2750840/99‑1            AGGGGGGCAACAAGGGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCA                                                                                      >  1:1020002/1‑99              GGGGGCAACAAGGGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAAa                                                                                    >  1:393131/1‑98                 GGCAACAAGGGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTA                                                                                 <  1:1033998/99‑1                   CAACAAGGGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACT                                                                               <  2:2210387/99‑1                   CAACAAGGGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACT                                                                               <  2:1156030/99‑1                     ACAAGGGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGA                                                                             >  2:2442915/1‑99                        AGGGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTT                                                                          >  1:934804/1‑99                          GGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAG                                                                        <  2:794831/99‑1                          GGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAG                                                                        <  2:1102301/99‑1                                 ATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGA                                                                 >  2:708112/1‑99                                  TATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGAT                                                                >  1:1750683/1‑99                                    TCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGG                                                              >  2:2685853/1‑99                                    TCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGG                                                              >  1:1212134/1‑99                                    TCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGG                                                              >  1:635420/1‑99                                          GCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTT                                                        >  2:2816597/1‑99                                          GCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTT                                                        <  2:790001/99‑1                                           CAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTT                                                       <  1:1719735/99‑1                                             GCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCGACTTACTGATTTAGTGTATGATGGTGTTTTTGA                                                     <  2:1700381/99‑1                                             GCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGA                                                     >  1:82499/1‑99                                                 AGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTG                                                 <  2:665561/99‑1                                                 AGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTG                                                 >  1:2799055/1‑99                                                   GACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCT                                               <  2:2671178/99‑1                                                    ACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTC                                              <  1:3062487/99‑1                                                           ATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGC                                       <  2:2277246/99‑1                                                              ATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTC                                    >  1:2601716/1‑99                                                              ATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTC                                    <  2:2572258/99‑1                                                              ATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTC                                    >  2:157686/1‑99                                                              ATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTC                                    <  1:242720/99‑1                                                                CGCGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTG                                  <  1:544691/99‑1                                                                  CGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTT                                <  2:193663/99‑1                                                                  CGACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTT                                <  1:1437650/99‑1                                                                    ACCGCAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTC                              <  2:1733122/99‑1                                                                        CAGATGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATC                          <  1:115766/99‑1                                                                            TGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCT                      >  1:2438632/1‑99                                                                            TGGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCT                      <  1:2504953/99‑1                                                                             GGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTG                     >  1:777214/1‑99                                                                             GGCCGCGTTGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTG                     <  2:496043/99‑1                                                                                     TGTTTATGCTGGTGGTGATGCTGCCCACTTACTGATTTCGTGTCTGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCT             <  2:2417285/99‑1                                                                                     TGTTTATGCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCT             >  1:728253/1‑99                                                                                            GCTGGTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGC      <  1:2462642/99‑1                                                                                                GTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACT  <  2:1666603/99‑1                                                                                                                                                                                                    TGGCGCTTCTGAGGGGGGCAACAAGGGGATTGATATCGCAGGCAGCAAAGGACAGGCAATTATCGCGACCGCAGATGGCCGCGTTGTTTATGCTGGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2867938‑2867842 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACT  >  NC_000913/3583428‑3583524

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ 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.