| New junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | = 2201286 | 162 (0.800) | 12 (0.070) | 10/136 | NT | 8.1% | intergenic (+16/+353) | kdpE/cshA | KDP operon transcriptional regulatory protein KdpE/DEAD‑box ATP‑dependent RNA helicase CshA |
| ? | USA300TCH1516_ALE | = 2201313 | 135 (0.780) | intergenic (+43/+326) | kdpE/cshA | KDP operon transcriptional regulatory protein KdpE/DEAD‑box ATP‑dependent RNA helicase CshA | |||||
TTTCACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ > USA300TCH1516_ALE/2201185‑2201286‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ataaaaaagatcACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGATGTG < USA300TCH1516_ALE/2201313‑2201224 TTTCACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATGCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAA < 1:3153581/91‑1 TTCACAATGTCATGAGGACGCAAGAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAAT > 2:2914152/1‑91 TTCACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAAT > 2:3948250/1‑91 TTCACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAAT > 1:1747978/1‑91 TTCACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAAT > 1:218888/1‑91 TCACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATA < 2:641491/91‑1 CACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAA > 1:1133121/1‑91 CACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAA > 2:2944051/1‑91 CACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAA > 2:2630705/1‑91 CACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAA > 2:1816220/1‑91 CACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAA > 2:1815718/1‑91 CACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAA > 2:1581919/1‑91 CACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAA < 2:1233818/91‑1 CACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAA > 1:664045/1‑91 CACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAA > 1:1709192/1‑91 CACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAA > 1:118748/1‑91 ACAATGTGATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAA < 2:3514998/91‑1 ACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAA > 1:270631/1‑91 CAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCGGTGGAAAGAGAAATAATTAAATAAAA < 2:2238329/91‑1 CAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAA > 2:1544792/1‑91 AATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAA < 2:2504097/91‑1 AATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAA > 2:3956249/1‑91 AATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAA > 2:62072/1‑91 AATGTCATGACGACGCAAAAGATATTATTAAAACACATCCACGCATGGGTTATCAAATGTTGCAGTGGAAAGAAAAATAATTAAATAAAAA < 2:331964/91‑1 ATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAA < 2:2596231/91‑1 ATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAA < 1:3952503/91‑1 ATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAA > 1:2167043/1‑91 ATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAA < 2:3106257/91‑1 ATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAA > 1:2167105/1‑91 ATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAA < 2:3106066/91‑1 TGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAG > 1:1082606/1‑91 GTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGA > 1:327604/1‑91 GTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGA > 2:1793844/1‑91 GTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGA > 1:326883/1‑91 GTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGA > 2:1628278/1‑91 GTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGA < 2:3774852/91‑1 GTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAAAAAAAAAAAAAAAAAGA < 2:3774833/91‑1 GTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGATGCAGTGGAAAGAGAAATAATTAAATAAAAAAGA < 2:441862/91‑1 TCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGAT < 1:1298806/91‑1 aATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATC < 2:3405365/90‑1 CATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATC < 1:2680059/91‑1 CATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATC < 1:2276116/91‑1 CATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATC > 1:1352970/1‑91 CATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATC > 2:2449417/1‑91 CATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATC < 1:3438957/91‑1 AAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATCACTGCCAATCATT < 2:21300/91‑1 ATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAGAGAATTATATAAAAAAGATCACTGCCAATCATTCGTTT < 2:1412046/91‑1 ATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATCACTGCCAATCATTCGTTTAAT < 2:105784/91‑1 tgAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATCACTGCCAATCATTCGTTTAATG < 2:1437041/89‑1 AAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAAATAAATAAAAAAGATCACTGCCAATCATTCGTTTAATGGC < 2:653294/91‑1 agCACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATCACTGCCAATCATTCGTTTAATGGCAG < 2:2532943/89‑1 ACACATCCAGGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATCACTGCCAATCATTCGTTTAATGGCAGC < 1:3790892/91‑1 ACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATCACTGCCAATCATTCGTTTAATGGCAGC < 2:919932/91‑1 ACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATGATTAAATATAAACGATCACTGCCAATCATTCGTTTAATGGCAGCGA < 1:3158366/91‑1 CATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATCACTGCCAATCATTCGTTTAATGGCAGCGAT < 2:3417438/91‑1 CATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATCACTGCCAATCATTCGTTTAATGGCAGCGAT < 2:2349025/91‑1 TTGGTTATCAAATGTTGCAGTGTAAAGAGAAATAATTAAATAAAAAAGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATT < 2:3191173/91‑1 gaagATAAAAAAGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAAC < 2:105199/87‑1 TAAATAAAAAAGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACC < 1:135293/91‑1 TAAATAAAAAAGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACC < 1:136240/91‑1 ATAAAAAAGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAAT < 1:338762/91‑1 ATAAAAAAGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAAT < 2:3708043/91‑1 AAAAAAGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGC < 1:427926/91‑1 AAAAAAGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGC > 1:1206882/1‑91 AAAAAGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCG > 1:3355144/1‑91 AAAAAGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCG < 2:515664/91‑1 AAAGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTG < 2:2328162/91‑1 AAAGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTG < 2:2023623/91‑1 AAAGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTG < 1:3318237/91‑1 AAGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGG > 1:2871522/1‑91 AGATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGA > 2:1587381/1‑91 GATCACTGTCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCCCTGCAACATTTGATAACCAATGCGTGGAT > 2:2450747/1‑91 GATCACTGTCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGAT > 2:2453293/1‑91 GATCACTGTCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAAACAATGCGTGGAT > 2:2450587/1‑91 GATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGAT < 2:3614423/91‑1 GATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGAT > 2:2891093/1‑91 ATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGATG > 2:792428/1‑91 ATCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCACTTTCCACTGCAACATTTGATAACCAATGCGTGGATG < 1:3351798/91‑1 ATCACTGCCAATCATTCGTTTAATGGCAGCGATCTCTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGCGGATG > 2:3205427/1‑91 TCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGATGT > 1:2556424/1‑91 TCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGATGT < 2:3335588/91‑1 TCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGATGT < 2:3335087/91‑1 TCACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATATAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGATGT < 2:3468925/91‑1 CACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGATGTG > 1:3537044/1‑91 CACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGATGTG < 2:3790335/91‑1 CACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGATGTG > 1:1409924/1‑91 CACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGATGTG > 2:713805/1‑91 CACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGATGTG > 2:181783/1‑91 CACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGATGTG > 2:2029849/1‑91 TTTCACAATGTCATGAGGACGCAAAAGATATTATTAAAACACATCCACGCATTGGTTATCAAATGTTGCAGTGGAAAGAGAAATAATTAAATAAAAAAGATC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ > USA300TCH1516_ALE/2201185‑2201286‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ataaaaaagatcACTGCCAATCATTCGTTTAATGGCAGCGATCTTTTTTATTTAATTATTTCTCTTTCCACTGCAACATTTGATAACCAATGCGTGGATGTG < USA300TCH1516_ALE/2201313‑2201224 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ 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. |