BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238511.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 = 3,442,711 number of mapped reads = 2,904,835 (84.38%) number of supplementary alignments = 24,956 (0.72%) number of secondary alignments = 0 number of mapped bases = 179,407,247 bp number of sequenced bases = 179,344,122 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 800,594 duplication rate = 19.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7964 >>>>>>> ACTG content number of A's = 44,653,184 bp (24.9%) number of C's = 32,474,571 bp (18.11%) number of T's = 58,544,142 bp (32.64%) number of G's = 43,659,846 bp (24.34%) number of N's = 12,379 bp (0.01%) GC percentage = 42.45% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 947,513 number of insertions = 11,225 mapped reads with insertion percentage = 0.38% number of deletions = 36,866 mapped reads with deletion percentage = 1.26% homopolymer indels = 43.89% >>>>>>> Coverage mean coverageData = 0.058X std coverageData = 0.731X There is a 2.59% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.72% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% 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 13761354 0.05521091159086821 0.8904109967744921 chr2 243199373 14960142 0.06151390036684017 1.504824804811458 chr3 198022430 11725089 0.05921091363235973 0.4926732905389621 chr4 191154276 11589484 0.06062895501223316 0.4976755459131214 chr5 180915260 11611103 0.06417978781889377 0.5103079804755908 chr6 171115067 10498292 0.061352236153465085 0.6777714427650361 chr7 159138663 9601916 0.06033678943249636 0.7436595074133856 chr8 146364022 8457968 0.05778720674948383 0.5954824003062696 chr9 141213431 7516003 0.05322442027486748 0.5523599520195476 chr10 135534747 8718974 0.06433017505097789 0.6067939267260465 chr11 135006516 8067774 0.05975840454989595 0.5688138333017273 chr12 133851895 7938101 0.05930510733523795 0.491711604713291 chr13 115169878 5734473 0.0497914307072549 0.5119523689290114 chr14 107349540 5214495 0.04857491704202924 0.5978586192493274 chr15 102531392 4745622 0.0462845759472377 0.6678016755372076 chr16 90354753 5308574 0.058752570548225615 0.5223004859171386 chr17 81195210 5256330 0.06473694692088364 0.54562208899166 chr18 78077248 4957433 0.06349395152861945 1.113245691778626 chr19 59128983 3712297 0.06278303484435035 0.6838604239744615 chr20 63025520 3615220 0.05736120860248357 0.4954458315564973 chr21 48129895 2551240 0.05300738761221067 0.46776209502383626 chr22 51304566 1988691 0.03876245634745258 0.38831290819852177 chrMT 16571 21336 1.287550540100175 2.2100310751927137 chrX 155270560 11335643 0.07300574558370886 0.5691278753152172 chrY 59373566 519693 0.008752935607741668 0.2518736407819287