BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063588.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,263,413 number of mapped reads = 3,884,074 (91.1%) number of supplementary alignments = 44,363 (1.04%) number of secondary alignments = 0 number of mapped bases = 258,922,697 bp number of sequenced bases = 258,811,547 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 519,198 duplication rate = 9.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1066 >>>>>>> ACTG content number of A's = 72,376,282 bp (27.96%) number of C's = 48,511,291 bp (18.74%) number of T's = 81,036,041 bp (31.31%) number of G's = 56,617,588 bp (21.88%) number of N's = 270,345 bp (0.1%) GC percentage = 40.62% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 2,067,679 number of insertions = 17,919 mapped reads with insertion percentage = 0.46% number of deletions = 63,462 mapped reads with deletion percentage = 1.62% homopolymer indels = 46.46% >>>>>>> Coverage mean coverageData = 0.0836X std coverageData = 0.6579X There is a 4.25% of reference with a coverageData >= 1X There is a 2.01% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% 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% 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 17404581 0.06982763344850403 0.6349501870940727 chr2 243199373 21272386 0.08746891794001459 0.7651990564128799 chr3 198022430 21488852 0.10851726241315188 0.5594177310100719 chr4 191154276 20712127 0.10835293582446463 0.5778155437953996 chr5 180915260 9596788 0.05304576297212297 0.3865954793365538 chr6 171115067 19367467 0.113183878775561 0.6143584189345835 chr7 159138663 16760797 0.10532196691887502 0.7718635068708515 chr8 146364022 14655127 0.10012793307907322 1.4077661509422699 chr9 141213431 8628840 0.06110495254520089 0.5180332676350875 chr10 135534747 7928468 0.05849767808988495 0.4992132210463469 chr11 135006516 17412058 0.1289719823597255 0.867432400892923 chr12 133851895 14278176 0.10667145205527348 0.5629273893294449 chr13 115169878 9846995 0.08549974325752085 0.5008383554735342 chr14 107349540 7630939 0.07108497157975711 0.4859260446958893 chr15 102531392 7222026 0.07043721790103075 0.4503882066710825 chr16 90354753 7219564 0.07990242638370114 0.4944829564900157 chr17 81195210 6730858 0.08289723002132761 0.5507618422398459 chr18 78077248 5530160 0.0708293407062708 0.9334141962032878 chr19 59128983 4438927 0.07507193215212242 0.5809758007562719 chr20 63025520 8889736 0.14104978427786077 0.6786713419593118 chr21 48129895 5227707 0.10861663005913476 0.5758437765264943 chr22 51304566 3420116 0.06666299447889297 0.42481759078926873 chrMT 16571 33769 2.037837185444451 2.614971008450977 chrX 155270560 2847443 0.0183385891053655 0.26576328345124695 chrY 59373566 378790 0.0063797751342744005 0.1506637337138216