BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514767.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 62,154,609 number of mapped reads = 61,660,303 (99.2%) number of supplementary alignments = 4,672,607 (7.52%) number of secondary alignments = 0 number of mapped bases = 5,868,534,688 bp number of sequenced bases = 5,863,870,352 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,726,888 duplication rate = 49.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.5126 >>>>>>> ACTG content number of A's = 1,716,907,032 bp (29.28%) number of C's = 1,208,117,215 bp (20.6%) number of T's = 1,699,177,594 bp (28.98%) number of G's = 1,232,103,369 bp (21.01%) number of N's = 7,565,142 bp (0.13%) GC percentage = 41.61% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 38,924,770 number of insertions = 2,825,308 mapped reads with insertion percentage = 4.42% number of deletions = 2,028,566 mapped reads with deletion percentage = 3.1% homopolymer indels = 42.65% >>>>>>> Coverage mean coverageData = 1.8957X std coverageData = 128.9348X There is a 3.99% of reference with a coverageData >= 1X There is a 1.88% of reference with a coverageData >= 2X There is a 1.25% of reference with a coverageData >= 3X There is a 1.02% of reference with a coverageData >= 4X There is a 0.88% of reference with a coverageData >= 5X There is a 0.8% of reference with a coverageData >= 6X There is a 0.74% of reference with a coverageData >= 7X There is a 0.7% of reference with a coverageData >= 8X There is a 0.66% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.6% of reference with a coverageData >= 11X There is a 0.58% of reference with a coverageData >= 12X There is a 0.56% of reference with a coverageData >= 13X There is a 0.54% of reference with a coverageData >= 14X There is a 0.53% of reference with a coverageData >= 15X There is a 0.51% of reference with a coverageData >= 16X There is a 0.5% of reference with a coverageData >= 17X There is a 0.48% of reference with a coverageData >= 18X There is a 0.47% of reference with a coverageData >= 19X There is a 0.46% of reference with a coverageData >= 20X There is a 0.45% of reference with a coverageData >= 21X There is a 0.44% of reference with a coverageData >= 22X There is a 0.43% of reference with a coverageData >= 23X There is a 0.42% of reference with a coverageData >= 24X There is a 0.42% of reference with a coverageData >= 25X There is a 0.41% of reference with a coverageData >= 26X There is a 0.4% of reference with a coverageData >= 27X There is a 0.39% of reference with a coverageData >= 28X There is a 0.39% of reference with a coverageData >= 29X There is a 0.38% of reference with a coverageData >= 30X There is a 0.38% of reference with a coverageData >= 31X There is a 0.37% of reference with a coverageData >= 32X There is a 0.36% of reference with a coverageData >= 33X There is a 0.36% of reference with a coverageData >= 34X There is a 0.35% of reference with a coverageData >= 35X There is a 0.35% of reference with a coverageData >= 36X There is a 0.34% of reference with a coverageData >= 37X There is a 0.34% of reference with a coverageData >= 38X There is a 0.34% of reference with a coverageData >= 39X There is a 0.33% of reference with a coverageData >= 40X There is a 0.33% of reference with a coverageData >= 41X There is a 0.32% of reference with a coverageData >= 42X There is a 0.32% of reference with a coverageData >= 43X There is a 0.32% of reference with a coverageData >= 44X There is a 0.31% of reference with a coverageData >= 45X There is a 0.31% of reference with a coverageData >= 46X There is a 0.3% of reference with a coverageData >= 47X There is a 0.3% of reference with a coverageData >= 48X There is a 0.3% of reference with a coverageData >= 49X There is a 0.3% of reference with a coverageData >= 50X There is a 0.29% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 471810888 1.892917602801078 89.61100803909162 chr2 243199373 446237719 1.8348637724489527 91.84750583049734 chr3 198022430 284482495 1.4366175336804017 62.56415746368599 chr4 191154276 285296515 1.4924935029965012 61.44157249456059 chr5 180915260 304179515 1.6813369695845448 103.2303320626547 chr6 171115067 350191558 2.046526726953857 95.34724690226273 chr7 159138663 425339253 2.6727587437378433 182.49510747782304 chr8 146364022 197104435 1.3466727157853042 72.3091500112425 chr9 141213431 144920454 1.0262512069407903 42.00953496214567 chr10 135534747 319581717 2.3579319995336694 127.63622708587936 chr11 135006516 315391682 2.336121924663251 144.01044990441838 chr12 133851895 346864705 2.5914067559521663 237.958296593747 chr13 115169878 256008732 2.2228792497288223 124.04206426686963 chr14 107349540 140358653 1.3074918905101969 81.25121090848037 chr15 102531392 207056233 2.019442328452929 89.73071650925931 chr16 90354753 99726084 1.1037170783921018 58.0582694809798 chr17 81195210 194016524 2.3895070164853323 54.0620518683579 chr18 78077248 210044254 2.690210776896235 75.1898464640334 chr19 59128983 114495529 1.9363689884535982 69.85087903672915 chr20 63025520 191934540 3.04534639301667 262.2728462603705 chr21 48129895 75355095 1.5656609057634554 63.65506028640426 chr22 51304566 184430546 3.5948173891579165 486.6481231735751 chrMT 16571 1787831 107.88914368475047 186.77466395699113 chrX 155270560 179702031 1.1573477354625372 98.92242594873491 chrY 59373566 122217700 2.0584530833132035 112.27255853467977