BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013215.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 = 3,602,850 number of mapped reads = 2,717,310 (75.42%) number of supplementary alignments = 16,766 (0.47%) number of secondary alignments = 0 number of mapped bases = 169,537,109 bp number of sequenced bases = 169,468,217 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 218,205 duplication rate = 6.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7997 >>>>>>> ACTG content number of A's = 47,372,087 bp (27.95%) number of C's = 31,877,714 bp (18.81%) number of T's = 52,434,782 bp (30.94%) number of G's = 37,724,054 bp (22.26%) number of N's = 59,580 bp (0.04%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,409,771 number of insertions = 12,477 mapped reads with insertion percentage = 0.45% number of deletions = 40,799 mapped reads with deletion percentage = 1.49% homopolymer indels = 44.74% >>>>>>> Coverage mean coverageData = 0.0548X std coverageData = 0.451X There is a 3.9% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 12904552 0.05177339959365638 0.5772381730053817 chr2 243199373 16681967 0.06859379115257834 0.8111740697669232 chr3 198022430 11665214 0.058908548895193334 0.3262958957957166 chr4 191154276 11043480 0.05777260248156834 0.3322127681746747 chr5 180915260 11027534 0.06095413952366428 0.33140856980616007 chr6 171115067 10221507 0.05973469887371169 0.42656670800433877 chr7 159138663 8833827 0.05551025020236597 0.5262486051430425 chr8 146364022 7775403 0.05312373145908767 0.5515363396497992 chr9 141213431 7210207 0.051058932205959924 0.3763629201080771 chr10 135534747 7263016 0.053587852272303275 0.40260301944878457 chr11 135006516 7356449 0.05448958478418923 0.35676439510131847 chr12 133851895 7904247 0.05905218600005625 0.33089848209813055 chr13 115169878 5271545 0.04577190747740481 0.30823183635285595 chr14 107349540 5096988 0.04748029660863009 0.30833633948854666 chr15 102531392 4874535 0.04754187868628566 0.29294974274557406 chr16 90354753 4461516 0.04937776765324122 0.32358840645656634 chr17 81195210 4258182 0.05244375868970596 0.3157077038082861 chr18 78077248 4554231 0.05832980947279289 0.587912143948486 chr19 59128983 3175020 0.05369650954422808 0.4556656581143874 chr20 63025520 3608009 0.05724679463176186 0.32640788670060633 chr21 48129895 2599976 0.054019980720922 0.3284508790534095 chr22 51304566 2003628 0.039053600024606 0.2596828298802286 chrMT 16571 320789 19.358457546315854 13.573217005005207 chrX 155270560 9025468 0.058127361684017886 0.34379631755085455 chrY 59373566 399819 0.006733956319888214 0.138463581986292