BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819001.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,127,079 number of mapped reads = 1,093,289 (97%) number of supplementary alignments = 18,838 (1.67%) number of secondary alignments = 0 number of mapped bases = 100,838,897 bp number of sequenced bases = 100,774,722 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 374,199 duplication rate = 28.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0877 >>>>>>> ACTG content number of A's = 30,119,056 bp (29.89%) number of C's = 22,314,730 bp (22.14%) number of T's = 27,988,138 bp (27.77%) number of G's = 20,347,985 bp (20.19%) number of N's = 4,813 bp (0%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 687,908 number of insertions = 16,641 mapped reads with insertion percentage = 1.47% number of deletions = 33,414 mapped reads with deletion percentage = 2.99% homopolymer indels = 40.86% >>>>>>> Coverage mean coverageData = 0.0326X std coverageData = 0.4704X There is a 1.9% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 10074287 0.040418302508461956 0.8070622588787874 chr2 243199373 8107541 0.03333701440093762 0.7571994776028266 chr3 198022430 5338786 0.026960511493571714 0.2534092219965235 chr4 191154276 5387542 0.028184260968349983 0.3284720890879729 chr5 180915260 5253444 0.029038147473021348 0.2732293621273473 chr6 171115067 4341405 0.0253712608487013 0.30274521115568986 chr7 159138663 5078106 0.031909945102404184 0.5246957230279375 chr8 146364022 9214273 0.06295449437704029 0.43762660042200285 chr9 141213431 4329381 0.030658422285625226 0.38438523006404607 chr10 135534747 5255957 0.03877940614003581 0.5980572935969097 chr11 135006516 3458282 0.025615667320827686 0.3028176044916181 chr12 133851895 4641633 0.03467737980101066 0.29421473565589706 chr13 115169878 2253312 0.019565115802241278 0.21886782949214567 chr14 107349540 2453209 0.022852533881374808 0.24637275586290833 chr15 102531392 2662275 0.0259654623629805 0.2505003925562274 chr16 90354753 3287748 0.03638710627652316 0.570381748883372 chr17 81195210 3478772 0.042844547110599256 0.3645842571808818 chr18 78077248 2263956 0.0289963601176107 0.47702688352944966 chr19 59128983 2038347 0.034472891238464226 0.6361673032270214 chr20 63025520 2974939 0.0472021333580429 0.3646414931391386 chr21 48129895 1428140 0.02967261823446737 0.30446179492958914 chr22 51304566 810031 0.015788672688508854 0.21964269451067636 chrMT 16571 123175 7.433166374992457 6.446186435342061 chrX 155270560 6125710 0.03945184457375564 0.35613617511682605 chrY 59373566 458646 0.007724750775454518 0.5558646312195054