BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525136.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 646,840 number of mapped reads = 553,843 (85.62%) number of supplementary alignments = 15,095 (2.33%) number of secondary alignments = 0 number of mapped bases = 42,158,350 bp number of sequenced bases = 42,141,445 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,917 duplication rate = 1.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2511 >>>>>>> ACTG content number of A's = 11,018,143 bp (26.15%) number of C's = 8,235,382 bp (19.54%) number of T's = 12,923,311 bp (30.67%) number of G's = 9,962,992 bp (23.64%) number of N's = 1,617 bp (0%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 325,674 number of insertions = 3,934 mapped reads with insertion percentage = 0.7% number of deletions = 9,843 mapped reads with deletion percentage = 1.75% homopolymer indels = 42.54% >>>>>>> Coverage mean coverageData = 0.0136X std coverageData = 0.1655X There is a 1.28% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 3444119 0.013817895362435226 0.21359419504763363 chr2 243199373 3554822 0.014616904460522601 0.2351704690456887 chr3 198022430 2751246 0.01389360791098261 0.12265159925580046 chr4 191154276 2399814 0.012554330722897352 0.12281531506768141 chr5 180915260 2553258 0.01411300517159249 0.12436345464338637 chr6 171115067 2417974 0.014130690198075896 0.13149116165489325 chr7 159138663 2363465 0.014851607745378633 0.2336590090843892 chr8 146364022 2198196 0.015018690863797115 0.21228987467880966 chr9 141213431 1801115 0.012754558735988788 0.16157042203976404 chr10 135534747 2004925 0.014792701092362684 0.16634406257189044 chr11 135006516 1923199 0.014245230948704727 0.16599687899895807 chr12 133851895 1945891 0.014537642518994595 0.12580264485635745 chr13 115169878 1327921 0.011530106856586234 0.11160370020950275 chr14 107349540 1282709 0.011948900759146243 0.12201945185974904 chr15 102531392 1227615 0.011973064795609134 0.11326986428920283 chr16 90354753 1264415 0.013993895816415988 0.12805899683676647 chr17 81195210 1214202 0.01495410874607012 0.14008193037809438 chr18 78077248 1155147 0.014794924636688014 0.23792928564626514 chr19 59128983 935132 0.015815120649039408 0.19481899244339299 chr20 63025520 899326 0.014269235700078318 0.12612828996032774 chr21 48129895 551953 0.011467986788668456 0.11509928036882477 chr22 51304566 515555 0.010048910656412141 0.10398326169157604 chrMT 16571 890 0.05370828555910929 0.23073266165013773 chrX 155270560 2320421 0.014944371940179774 0.14662715766562978 chrY 59373566 105040 0.0017691374643052432 0.05717877255625437