New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_hsa_tpiA	1434744 =	2 (0.040)	48 (0.970)	38/282	0.4	96.0%	intergenic (‑520/+214)	ynaE/ttcC	cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
	?	NC_000913_3_hsa_tpiA	= 1469240	NA (NA)					intergenic (‑91/‑1)	insC1/ydbA	IS2 repressor TnpA/pseudogene, autotransporter homolog; interrupted by IS2 and IS30

GCGACAACAATAAGCTACGATAATCCACTCTTTTTTTGCCCCTTTTTTGCCCCTTTTGCAGCGTTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_hsa_tpiA/1434887‑1434744 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGAT  <  NC_000913_3_hsa_tpiA/1469240‑1469094                                                                                                                                                                                                                                                                                                      GCGACAACAAGAAGCTACGATAATCCACTCTTTTTTTGCCCCTTTTTTGCCCCTTTTGCAGCGTTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGAC                                                                                                                                                 >  1:847523/1‑149                   GATAATCCACTCTTTTTTTGCCCCTTTTTTGCCCCTTTTGCAGCGTTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCA                                                                                                                               <  1:15009/149‑1                             TCTTTTTTTGCCCCTTTTTTGCCCCTTTTGCAGCGTTTTTCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAAT                                                                                                                     >  2:349169/1‑149                             TCTTTTTTTGCCCCTTTTTTGCCCCTTTTGCAGCGTTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAAT                                                                                                                     >  1:590780/1‑149                               TTTTTTTGCCCCTTTTTTGCCACTTTTACAGCGATTTGCCCCATTTTTGCCACCGAAAAAAATTCCACAACGTCTCAATCAAAGTCAAACCAACTGCAACACGTTCTTCCATACTATACTGTCCCCCTTAAGCTCCAGAAAACCAATAT                                                                                                                   >  2:240500/1‑149                                    TTGCCCCCTGTTTGCCCCTTTTGCAGCGTTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTT                                                                                                              <  2:692470/149‑1                                       CCCCTTTTTTGCCCCTTTTGCAGCGTTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAA                                                                                                           <  1:349169/149‑1                                          cgTTTTTGCTCCTTTTGCAGCGGTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGGATACTAGTCTTGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAA                                                                                                        <  2:751684/147‑1                                          CTTTTTTGCCCCTTTTGCAGCGTTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAA                                                                                                        <  1:866171/149‑1                                          CTTTTTTGCCCCTTTTGCAGCGTTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAA                                                                                                        <  1:866173/149‑1                                            TTTTTGCCCCTTTTGTAGCGTTTTTCCCCATGTCTGCCACCGAAAAACATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGT                                                                                                      <  2:44842/149‑1                                                TGCCCCTTTTGCAGCGTTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTTAATAAGTGATA                                                                                                  <  1:546421/149‑1                                                    CCTTTTGCAGCGTTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGAACGGTCTTGCATACTAGACTATCCTCCTGAATGTCCAGACAACCAATATCACTTAATTAAGTGCTAGTCT                                                                                              >  1:165773/1‑149                                                         TGCAGCGTTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATA                                                                                         <  1:20132/149‑1                                                          GCAGCGTTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATAC                                                                                        >  1:713090/1‑149                                                           CAGCGTTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACT                                                                                       <  2:423235/149‑1                                                                tttgcCCCCATGTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTT                                                                                  <  1:808248/144‑1                                                                 TTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTT                                                                                 <  1:423176/149‑1                                                                  tgGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTT                                                                                <  2:113968/147‑1                                                                   TGCCCCATTTTTGCCACCGAAAAAAATTCCAAAATTTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTA                                                                               <  1:457559/149‑1                                                                    GCCCCATTTTTGCCACCGAAAAAAATTCCACCACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTA                                                                               >  2:624959/1‑148                                                                    GCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTA                                                                               <  1:624959/148‑1                                                                     CCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGA                                                                             <  2:812491/149‑1                                                                      CCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGAC                                                                            <  1:481686/149‑1                                                                        CATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTA                                                                          >  1:273262/1‑149                                                                        CATTTATGCCACCGAAAAAAATTCCAAACCTTCTCAATCAAAGTCAACTCAACCGCAGCACGTTCTTGCATACTATACTGGCTCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTA                                                                          <  2:655239/149‑1                                                                               GCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGAACGTTCTTTCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTG                                                                   <  1:638263/149‑1                                                                                 CACAGAAATAAATTCCAAAACGGCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGA                                                                 <  2:614341/149‑1                                                                                  ACCGAAAAAAATTCCAAACCGGCTTAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAACTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAG                                                                >  2:446196/1‑149                                                                                      AAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATAACTTAAATAAGTGATAGTCTTATTACTAGTTTTTATACTTGTCTTTGGTGAACA                                                            >  2:865581/1‑149                                                                                           AATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGA                                                      <  2:590780/149‑1                                                                                             TTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCAATTAAATAAGTGATAGTCTTAATACTAATTTTTCGACTAATAATTGGA‑AACACGATGATT                                                    >  2:243176/1‑149                                                                                                 AAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATG                                                <  1:615891/149‑1                                                                                                 AAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATG                                                <  1:615750/149‑1                                                                                                        CTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATGTCTTCGG                                         >  2:345836/1‑149                                                                                                           AATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATGTCTTAGGGCC                                      >  2:731906/1‑149                                                                                                           AATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATAATTGATGTCTTAGGGCC                                      >  1:72302/1‑149                                                                                                            ATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATGTCTTAG                                          <  2:546333/144‑1                                                                                                            ATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATGTCTTAG                                          >  1:546333/1‑144                                                                                                             TCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATGTCTTAGGGCCGG                                    >  1:709719/1‑149                                                                                                             TCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCA                                                                                                                 >  2:272390/1‑73                                                                                                             TCAAAGTCAAACCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCA                                                                                                                 <  1:272390/73‑1                                                                                                                        CCAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATGTCTTAGGGCCGGAGAAACGCCGA                         >  2:854088/1‑149                                                                                                                         CAACCGCAGCACGTTCTTGCATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATGTCTTAGGGCCGGAGAAACGCAGAC                        >  2:475861/1‑149                                                                                                                                             ATACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAG    >  1:227555/1‑149                                                                                                                                               ACTAGACTGGCCCCCTGAATCTCCATACCGACAATAACACCTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGAT  <  1:161175/149‑1                                                                                                                                               ACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGAT  <  1:627617/149‑1                                                                                                                                               ACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATGTATTAGGGCCGGAGAAACGCCAACGGCGAACAACACAGGAAAAGAT  >  2:605553/1‑149                                                                                                                                                                                                                                                                                                      GCGACAACAATAAGCTACGATAATCCACTCTTTTTTTGCCCCTTTTTTGCCCCTTTTGCAGCGTTTTGCCCCATTTTTGCCACCGAAAAAAATTCCAAAACGTCTCAATCAAAGTCAAACCAACCGCAGCACGTTCTTGCATAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_hsa_tpiA/1434887‑1434744 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA‑GATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGAT  <  NC_000913_3_hsa_tpiA/1469240‑1469094

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ 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.