BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240066.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 = 2,577,943 number of mapped reads = 2,105,278 (81.67%) number of supplementary alignments = 18,814 (0.73%) number of secondary alignments = 0 number of mapped bases = 138,030,091 bp number of sequenced bases = 137,977,515 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 418,037 duplication rate = 12.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3068 >>>>>>> ACTG content number of A's = 37,947,489 bp (27.5%) number of C's = 24,658,222 bp (17.87%) number of T's = 45,028,948 bp (32.63%) number of G's = 30,330,223 bp (21.98%) number of N's = 12,633 bp (0.01%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,124,318 number of insertions = 10,041 mapped reads with insertion percentage = 0.47% number of deletions = 31,037 mapped reads with deletion percentage = 1.46% homopolymer indels = 49.08% >>>>>>> Coverage mean coverageData = 0.0446X std coverageData = 0.6306X There is a 1.8% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 12901926 0.051762864013085046 1.0473800011873287 chr2 243199373 11579681 0.0476139426560117 0.782161950022321 chr3 198022430 8702968 0.043949405125469874 0.4196677633631512 chr4 191154276 4616546 0.0241508905612972 0.3090982687979864 chr5 180915260 7858883 0.04343958049752133 0.42137101712210123 chr6 171115067 12259540 0.0716450059888648 0.6283994472695066 chr7 159138663 7777613 0.04887318300518837 0.5775680043276735 chr8 146364022 9828912 0.06715388020698147 1.073532704488777 chr9 141213431 3518072 0.024913154330199652 0.5159425163046929 chr10 135534747 6842442 0.050484780851068396 0.5132800681051429 chr11 135006516 4009388 0.029697736959599787 0.42041958477286917 chr12 133851895 6100465 0.04557623184938846 0.43491828021989215 chr13 115169878 5367239 0.04660280181941323 0.4393455414957104 chr14 107349540 4029264 0.0375340592982513 0.40008825901280387 chr15 102531392 3210582 0.031313161143857286 0.3526253859860941 chr16 90354753 3777211 0.041804231372310874 0.4207975546758125 chr17 81195210 2622546 0.032299269870722666 0.40402256811660314 chr18 78077248 6766171 0.08665995758457061 0.9643038934313054 chr19 59128983 2579632 0.04362720055577482 0.7003369100720066 chr20 63025520 2490269 0.03951207383929557 0.3993532026576016 chr21 48129895 2060387 0.042808882088772475 0.42231187147218485 chr22 51304566 708302 0.013805827730810549 0.2138978789730288 chrMT 16571 907247 54.7490797175789 36.915497937575026 chrX 155270560 7141900 0.04599648510316444 0.4618314109406945 chrY 59373566 372905 0.006280656950940087 0.1633460415965423