Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	1,638,416	IS1 (–) +9 bp	coding (21‑29/189 nt)	ynfQ ←	Qin prophage; protein YnfQ

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1638416 =	0 (0.000)	51 (0.920)	40/274	0.3	100%	coding (29/189 nt)	ynfQ	Qin prophage; protein YnfQ
	?	NC_000913	= 1979270	NA (NA)					noncoding (1/768 nt)	IS1	repeat region
*	?	NC_000913	= 1638424	0 (0.000)	48 (0.860)	34/276	0.5	100%	coding (21/189 nt)	ynfQ	Qin prophage; protein YnfQ
	?	NC_000913	1978503 =	NA (NA)					noncoding (768/768 nt)	IS1	repeat region

GTATTGTGAAATATTATCAAATGTAATCATCATTGATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1638295‑1638424 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGT  >  NC_000913/1978503‑1978636                                                                                                                                                                                                                                                                          GTATTGTGAAATATTATCAAATGTAATCATCATTGATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACT                                                                                                                              <  2:725072/140‑1   ATTGTGAAATATTATCAAATGTAATCATCATTGATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCC                                                                                                                            <  1:98784/140‑1   ATTGTGAAATATTATCAAATGTAATCATCATTGATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCC                                                                                                                            <  2:445115/140‑1     TGTGAAATATTATCAAATGTAATCATCATTGATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAA                                                                                                                          >  2:98726/1‑140       TGAAATATTATCAAATGTAATCATCATTGATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACT                                                                                                                        >  2:681650/1‑140              TTATCAAATGTAATCATCATTGATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGAT                                                                                                                 >  1:352660/1‑140               TATCAAATGTAATCATCATTGATTTATAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATA                                                                                                                <  1:792488/140‑1               TATCAAATGTAATCATCATTGATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATA                                                                                                                <  2:838473/140‑1                    AATGTAATCATCATTGATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTT                                                                                                           <  1:487999/140‑1                           TCATCATTGATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                                                                                    <  1:305072/140‑1                           TCATCATTGATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                                                                                    >  2:305072/1‑140                               CATTGATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                                                                                    <  2:898248/136‑1                               CATTGATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                                                                                    >  1:898248/1‑136                                   GATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAAT                                                                                            <  1:102063/140‑1                                       TACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCC                                                                                        <  2:703431/140‑1                                       TACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCC                                                                                        >  1:465242/1‑140                                          AAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGAT                                                                                     <  2:352660/140‑1                                                 ACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTG                                                                              <  1:98726/140‑1                                                         CCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAG                                                                      >  1:164933/1‑140                                                         CCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATG                                                                         <  1:925534/137‑1                                                         CCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATG                                                                         >  2:925534/1‑137                                                              AAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCA                                                                 <  2:799627/140‑1                                                               AAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCAC                                                                <  1:643551/140‑1                                                               AAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCAC                                                                <  2:465242/140‑1                                                                        TGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGA                                                       >  1:389060/1‑140                                                                                ACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACA                                               <  1:681650/140‑1                                                                                   TCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCG                                            >  2:3445/1‑140                                                                                            GATGTTCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTC                                   >  1:484624/1‑140                                                                                                 TCTATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGC                              >  2:121927/1‑140                                                                                                    ATACTGGGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCAATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGT                           >  1:554370/1‑140                                                                                                          GGAACCATGACAACACGGGCGTCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGG                     >  2:770116/1‑140                                                                                                          GGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGG                     >  2:274932/1‑140                                                                                                          GGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGG                     >  1:52616/1‑140                                                                                                          GGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGG                     >  1:714558/1‑140                                                                                                          GGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGG                     >  1:904616/1‑140                                                                                                          GGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCA                                <  2:771160/129‑1                                                                                                          GGAACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCA                                >  1:771160/1‑129                                                                                                             ACCATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCAACTTCCGTCCCAGCCGTGCCAGGTGC                  >  2:255658/1‑140                                                                                                               CATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTG                >  1:145897/1‑140                                                                                                               CATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTG                >  1:477272/1‑140                                                                                                               CATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTG                >  2:435662/1‑140                                                                                                               CATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCC                        >  1:326869/1‑132                                                                                                               CATGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCC                        <  2:326869/132‑1                                                                                                                 TGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCC              >  2:411110/1‑140                                                                                                                 TGACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCC              >  1:586262/1‑140                                                                                                                  GACAACACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCT             <  1:347360/140‑1                                                                                                                        ACGGGCATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCAACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATT       <  1:255658/140‑1                                                                                                                             CATCTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGT  >  2:714124/1‑140                                                                                                                                                                                                                                                                          GTATTGTGAAATATTATCAAATGTAATCATCATTGATTTACAAAAGATACATTTTGCCCCGAAAGGATTCATGTCAGAAACATCAAAAGATGATGTTCTATACTGGGAACCATGACAACACGGGCATCTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1638295‑1638424 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGT  >  NC_000913/1978503‑1978636

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ 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.