New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	376748 =	NA (NA)	13 (0.040)	9/94	NT	NA	intergenic (‑33/‑59)	yaiX/insC1	pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
	?	CP009273	376768 =	NA (NA)					intergenic (‑53/‑39)	yaiX/insC1	pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA

TAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAG  >  CP009273/376701‑376780                                                                    |             tAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAg              >  1:9373904/1‑68 (MQ=255) tAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAg              >  1:32671011/1‑68 (MQ=255) tAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAg              >  1:21067612/1‑68 (MQ=255) tAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAg              >  1:14393722/1‑68 (MQ=255) tAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAg              >  1:26175988/1‑68 (MQ=255) tAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAg              >  1:22921832/1‑68 (MQ=255) tAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAg              <  1:9146914/68‑1 (MQ=255)  aaaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGt             <  1:7918682/68‑1 (MQ=255)  aaaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGt             <  1:29947761/68‑1 (MQ=255)  aaaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGt             <  1:17136412/68‑1 (MQ=255)  aaaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGt             <  1:13903413/68‑1 (MQ=255)   aaCGCATTATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:6883654/68‑1 (MQ=255)   aaCGCATAATTTCTAGACTGGCCCCCTGAATCTCCAGACAAACAATATCACTTAAATAAGTGATAGTc            <  1:33854953/68‑1 (MQ=14)   aaCGCATAATTACTAGACTTCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:11134334/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTGCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:17437359/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:25815995/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:10622324/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:26850179/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:27484096/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:27875077/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:28003948/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:28292454/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:28485417/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:28811570/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:24425910/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:29607125/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:25676446/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:25134657/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:3919374/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:9191792/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:7114151/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:6535044/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:6464172/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:6270759/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:5738445/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:4443014/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:4347207/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:30662630/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:34524576/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:34111718/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:33667380/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:3352034/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:33111646/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:32168480/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:31520362/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:17065644/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:10070771/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:10881414/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:12134957/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:12374747/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:13338799/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:15377554/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:16627594/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:16988751/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:23982382/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:17896515/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:18768786/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:19511450/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:1971007/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:20300446/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:20515944/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:20832600/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:21423545/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:23826361/68‑1 (MQ=255)   aaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:20973956/68‑1 (MQ=255)    aCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCt           <  1:21798598/68‑1 (MQ=255)    aCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCt           <  1:19329024/68‑1 (MQ=255)     cGCATAATTACTAGACTGGCCCCCTGAATCTCCAGCCAACCAATATCACTTAAATAAGTGATAGTCtt          >  1:18925037/1‑68 (MQ=255)     cGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCtt          >  1:13091143/1‑68 (MQ=255)     cGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCtt          >  1:15266852/1‑68 (MQ=255)     cGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCtt          >  1:33695500/1‑68 (MQ=255)     cGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCtt          >  1:31809996/1‑68 (MQ=255)     cGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCtt          >  1:29747110/1‑68 (MQ=255)     cGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACGTAAATAAGTGATAGTCtt          >  1:12223056/1‑68 (MQ=255)      gCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTa         <  1:30689618/68‑1 (MQ=255)      gCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTa         <  1:25837782/68‑1 (MQ=255)      gCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTa         <  1:7397440/68‑1 (MQ=255)      gCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTa         <  1:7243393/68‑1 (MQ=255)      gCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTa         <  1:13895022/68‑1 (MQ=255)      gCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTa         >  1:13567628/1‑68 (MQ=255)        aTAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAAt       <  1:11681988/68‑1 (MQ=40)        aTAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAAt       <  1:29848070/68‑1 (MQ=40)        aTAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAAt       <  1:7160538/68‑1 (MQ=40)        aTAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAAt       <  1:19635381/68‑1 (MQ=40)           aTTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACt    <  1:24576372/68‑1 (MQ=35)            ttACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:16393306/59‑1 (MQ=33)            ttACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTa   >  1:15509772/1‑68 (MQ=33)            ttACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTa   >  1:15301355/1‑68 (MQ=33)            ttACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTa   >  1:15549026/1‑68 (MQ=33)            ttACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTa   >  1:1607047/1‑68 (MQ=33)            ttACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTa   >  1:27379729/1‑68 (MQ=33)             tACTAGACTGGCCCCCTGAATCTCGAGAAAACCAATATCACTTAAATAAGTGATAGTCTTTATACTAg  <  1:28023553/68‑1 (MQ=11)             tACTAGACTGGCCCCCTGAATCTCCAGACACCCACTATCACTTAAATAAGTGATAGTCTTAATACTAg  <  1:23989061/68‑1 (MQ=255)             tACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc            <  1:22756527/58‑1 (MQ=31)             tACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAg  <  1:21754875/68‑1 (MQ=31)             tACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAg  <  1:8313474/68‑1 (MQ=31)             tACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTAATAGTCTTAATACTAg  <  1:15445676/68‑1 (MQ=14)                                                                    |             TAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAG  >  CP009273/376701‑376780

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.