BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751188.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 5,468,408 number of mapped reads = 4,962,665 (90.75%) number of supplementary alignments = 180,857 (3.31%) number of secondary alignments = 0 number of mapped bases = 487,776,990 bp number of sequenced bases = 487,630,206 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 164,573 duplication rate = 1.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.1545 >>>>>>> ACTG content number of A's = 142,238,846 bp (29.17%) number of C's = 101,904,617 bp (20.9%) number of T's = 142,879,081 bp (29.3%) number of G's = 100,605,029 bp (20.63%) number of N's = 2,633 bp (0%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 1,813,765 number of insertions = 122,870 mapped reads with insertion percentage = 2.42% number of deletions = 66,810 mapped reads with deletion percentage = 1.32% homopolymer indels = 48.43% >>>>>>> Coverage mean coverageData = 0.1576X std coverageData = 1.5389X There is a 11.91% of reference with a coverageData >= 1X There is a 2.56% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.06% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 58966217 0.2365740023572499 4.44300833624854 chr2 243199373 36272647 0.14914778172557214 0.604675840273322 chr3 198022430 32150666 0.1623587085563994 0.5332731317984208 chr4 191154276 22233590 0.11631228170904218 0.49403667646819205 chr5 180915260 40029810 0.22126276136131356 0.578824301695926 chr6 171115067 27286466 0.15946267314964147 0.9205969695821641 chr7 159138663 27393376 0.17213526545714414 0.8230851193196415 chr8 146364022 24109144 0.16472042562481645 0.6397801258730104 chr9 141213431 21380651 0.151406639216917 0.6851536486541417 chr10 135534747 24163634 0.17828368396186994 1.9545726809969903 chr11 135006516 21724918 0.16091755156469634 0.7511976330093113 chr12 133851895 25383828 0.18964115524849312 0.5326379714790423 chr13 115169878 14267113 0.12387885832439624 0.42452765214692645 chr14 107349540 10337495 0.0962975248892543 0.3947367160948883 chr15 102531392 11875178 0.11581992371663109 0.4104347502662367 chr16 90354753 13774035 0.15244394503518813 0.9379172311030708 chr17 81195210 13715919 0.16892522354459086 0.7317775894301525 chr18 78077248 9984176 0.12787561364867778 1.4013610570298733 chr19 59128983 9447449 0.15977695743557774 3.164812399288839 chr20 63025520 8623876 0.136831493020605 0.4611845187417273 chr21 48129895 6128578 0.12733412362524374 0.4863944093111696 chr22 51304566 5591143 0.10897944249250642 0.4077754138353391 chrMT 16571 1263454 76.24488564359423 31.491583306238216 chrX 155270560 20499723 0.1320258199622646 0.5047188152711922 chrY 59373566 1173904 0.01977149224959808 0.7576859653803143