BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237568.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 = 1,452,206 number of mapped reads = 1,117,869 (76.98%) number of supplementary alignments = 5,951 (0.41%) number of secondary alignments = 0 number of mapped bases = 69,548,218 bp number of sequenced bases = 69,504,364 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,289 duplication rate = 6.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3817 >>>>>>> ACTG content number of A's = 18,638,693 bp (26.82%) number of C's = 11,810,942 bp (16.99%) number of T's = 22,981,814 bp (33.07%) number of G's = 15,937,653 bp (22.93%) number of N's = 135,262 bp (0.19%) GC percentage = 39.92% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 709,392 number of insertions = 5,826 mapped reads with insertion percentage = 0.52% number of deletions = 27,764 mapped reads with deletion percentage = 2.45% homopolymer indels = 49.41% >>>>>>> Coverage mean coverageData = 0.0225X std coverageData = 0.2347X There is a 1.69% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 5668850 0.02274357422764455 0.30446083868408913 chr2 243199373 6098239 0.025075060534798337 0.25991373999135503 chr3 198022430 4927566 0.02488387805361241 0.20598577266268886 chr4 191154276 4654765 0.02435082854228173 0.20576031991568433 chr5 180915260 4220299 0.02332749045050152 0.1962395275783882 chr6 171115067 4082891 0.02386049967183778 0.2145678296774463 chr7 159138663 3951581 0.024831055668728348 0.28209557719502537 chr8 146364022 3656311 0.024980941012949207 0.3536128949603539 chr9 141213431 2956940 0.02093950964196883 0.22679025205080713 chr10 135534747 3346005 0.024687433105253814 0.23377871518017926 chr11 135006516 3021718 0.02238201599099113 0.22764543748979352 chr12 133851895 3500783 0.026154153439516117 0.21189940641120222 chr13 115169878 2399848 0.020837462378834853 0.19005929310715855 chr14 107349540 2037489 0.01897995091548599 0.18348957115863254 chr15 102531392 1904016 0.01857007851800159 0.17463866247666476 chr16 90354753 1693324 0.018740840340740018 0.18431963724084394 chr17 81195210 1492873 0.018386220073819626 0.17883523158002174 chr18 78077248 1807072 0.02314466821371573 0.3317713300061651 chr19 59128983 1030112 0.01742143949947524 0.217469534603113 chr20 63025520 1290919 0.020482480747481338 0.19103510640481727 chr21 48129895 932644 0.019377644601136154 0.1881568099260016 chr22 51304566 608854 0.011867442753535816 0.13879958447981605 chrMT 16571 50817 3.066622412648603 2.922649008521545 chrX 155270560 4014227 0.025853110853725266 0.2167034854771423 chrY 59373566 200075 0.003369765595686134 0.0801247694123497