BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472698.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,260,590 number of mapped reads = 16,145,288 (99.29%) number of supplementary alignments = 118,593 (0.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,107,851 number of mapped paired reads (second in pair) = 8,037,437 number of mapped paired reads (both in pair) = 16,068,352 number of mapped paired reads (singletons) = 76,936 number of mapped bases = 1,587,733,794 bp number of sequenced bases = 1,587,416,528 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,001,436 duplication rate = 48.28% >>>>>>> Insert size mean insert size = 27,404.5674 std insert size = 1,605,910.8449 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 54.498 >>>>>>> ACTG content number of A's = 426,276,881 bp (26.85%) number of C's = 367,428,085 bp (23.15%) number of T's = 431,511,039 bp (27.18%) number of G's = 361,835,412 bp (22.79%) number of N's = 365,111 bp (0.02%) GC percentage = 45.94% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 6,589,705 number of insertions = 103,545 mapped reads with insertion percentage = 0.64% number of deletions = 84,680 mapped reads with deletion percentage = 0.52% homopolymer indels = 47.85% >>>>>>> Coverage mean coverageData = 0.5129X std coverageData = 31.1534X There is a 3.08% of reference with a coverageData >= 1X There is a 1.5% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.23% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.18% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.17% of reference with a coverageData >= 20X There is a 0.16% of reference with a coverageData >= 21X There is a 0.16% of reference with a coverageData >= 22X There is a 0.16% of reference with a coverageData >= 23X There is a 0.15% of reference with a coverageData >= 24X There is a 0.15% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.14% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.14% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.13% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.12% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.12% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 187315752 0.7515156882999301 32.5153073234751 chr2 243199373 108807618 0.447400898521231 22.699931201268974 chr3 198022430 175149346 0.8844924587583336 41.003357355929296 chr4 191154276 50706334 0.26526392744674987 37.60093947183336 chr5 180915260 69559855 0.38448859980081285 16.97403110887015 chr6 171115067 121529924 0.7102233960496301 30.523101453736345 chr7 159138663 73207875 0.460025700982545 33.192724970572776 chr8 146364022 72339591 0.4942443505686117 38.4092417268755 chr9 141213431 68088440 0.4821668839701232 29.451238121968895 chr10 135534747 31668137 0.23365327121612586 21.760719885032852 chr11 135006516 49991146 0.3702869126702003 23.0643910754435 chr12 133851895 79216714 0.5918236271514871 31.503303493486804 chr13 115169878 22963234 0.1993857630030658 11.709545250195692 chr14 107349540 49782776 0.46374466066645464 25.669565947136583 chr15 102531392 37082528 0.3616699946880659 19.20497942090322 chr16 90354753 90476365 1.001345939156073 53.78981699020093 chr17 81195210 97707009 1.2033592745187802 60.395936502759554 chr18 78077248 14927422 0.19118786051475584 8.722301752769916 chr19 59128983 48940310 0.8276873289026466 34.37315737258255 chr20 63025520 28911692 0.45872992400538704 23.35704327215403 chr21 48129895 13189177 0.2740329477136819 21.615259422509812 chr22 51304566 20683622 0.4031536296399038 18.428047756654383 chrMT 16571 5526 0.3334741415726269 0.8130855268449546 chrX 155270560 73943477 0.4762234193011219 34.58668634735041 chrY 59373566 1539924 0.025936188505167435 2.42160454976565