BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234053.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 = 1,671,186 number of mapped reads = 1,433,693 (85.79%) number of supplementary alignments = 13,233 (0.79%) number of secondary alignments = 0 number of mapped bases = 93,632,492 bp number of sequenced bases = 93,581,717 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,510 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8889 >>>>>>> ACTG content number of A's = 26,386,963 bp (28.2%) number of C's = 17,217,728 bp (18.4%) number of T's = 29,535,952 bp (31.56%) number of G's = 20,422,835 bp (21.82%) number of N's = 18,239 bp (0.02%) GC percentage = 40.22% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 730,611 number of insertions = 6,958 mapped reads with insertion percentage = 0.48% number of deletions = 29,107 mapped reads with deletion percentage = 2.01% homopolymer indels = 45.04% >>>>>>> Coverage mean coverageData = 0.0302X std coverageData = 0.3246X There is a 2.54% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 12956324 0.051981110209550895 0.7350568037620961 chr2 243199373 6124721 0.02518395061816216 0.2953907749232411 chr3 198022430 5235988 0.026441388483112747 0.18654888393927493 chr4 191154276 672960 0.003520507174006403 0.09747843927030064 chr5 180915260 9837455 0.05437603770958845 0.26991186707339976 chr6 171115067 8860883 0.05178318400214284 0.30999505997315613 chr7 159138663 5019416 0.03154114723208401 0.3338288793555951 chr8 146364022 5839646 0.039898097361659 0.39841891659655543 chr9 141213431 3961902 0.028056127324036197 0.23751813515789522 chr10 135534747 2144472 0.015822304224318212 0.19955989013566616 chr11 135006516 5633209 0.0417254601251987 0.3480698580292955 chr12 133851895 2034975 0.015203184086411328 0.14493542823396593 chr13 115169878 4768742 0.04140615656465313 0.23434138470381943 chr14 107349540 3684053 0.03431829330614738 0.22157090649975542 chr15 102531392 738727 0.007204886089910883 0.09853002153718703 chr16 90354753 1092512 0.012091361701802228 0.14742739582497957 chr17 81195210 984698 0.012127538065361244 0.16460629884661312 chr18 78077248 1480028 0.01895594475870871 0.4283395087948166 chr19 59128983 2884140 0.04877709464409358 0.4396395288110572 chr20 63025520 2563023 0.0406664316296002 0.2390501207227922 chr21 48129895 1829704 0.03801595661075097 0.23321347799291237 chr22 51304566 756901 0.014753092346595428 0.13804586261092738 chrMT 16571 50530 3.049302999215497 2.721496087746912 chrX 155270560 4232973 0.027261916231898692 0.21423824944664743 chrY 59373566 244510 0.004118162618024324 0.10516359335962776