BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230344.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 = 3,950,889 number of mapped reads = 3,766,903 (95.34%) number of supplementary alignments = 33,618 (0.85%) number of secondary alignments = 0 number of mapped bases = 271,313,631 bp number of sequenced bases = 271,200,589 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 229,437 duplication rate = 5.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6064 >>>>>>> ACTG content number of A's = 80,262,842 bp (29.6%) number of C's = 55,586,670 bp (20.5%) number of T's = 79,002,355 bp (29.13%) number of G's = 56,127,862 bp (20.7%) number of N's = 220,860 bp (0.08%) GC percentage = 41.19% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 2,382,777 number of insertions = 21,342 mapped reads with insertion percentage = 0.56% number of deletions = 67,796 mapped reads with deletion percentage = 1.78% homopolymer indels = 47.92% >>>>>>> Coverage mean coverageData = 0.0876X std coverageData = 0.7783X There is a 3.24% of reference with a coverageData >= 1X There is a 1.83% of reference with a coverageData >= 2X There is a 1.2% of reference with a coverageData >= 3X There is a 0.81% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% 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 14238433 0.057124964996576676 0.8838474307959069 chr2 243199373 30700858 0.12623740604791772 0.9033494778847703 chr3 198022430 25728105 0.12992520594762927 0.7718821675253418 chr4 191154276 11644156 0.060914964831861776 0.5302565144443775 chr5 180915260 17715623 0.0979222150746156 0.6703666615386267 chr6 171115067 24956531 0.1458464846932503 1.0569700347795516 chr7 159138663 12402769 0.07793686817640287 0.8231213467349365 chr8 146364022 15306761 0.10458007911261143 0.9262717002931361 chr9 141213431 9877831 0.0699496565592263 0.672502026380999 chr10 135534747 15119336 0.11155320930358914 0.8911027110821045 chr11 135006516 13187143 0.09767782615766486 0.9757141540280824 chr12 133851895 10837555 0.08096676554336418 0.6131456157073458 chr13 115169878 11307309 0.09817939548394763 0.6710246425007818 chr14 107349540 6466434 0.06023718406245616 0.5475102486289151 chr15 102531392 9238830 0.09010733025062218 0.640291640624973 chr16 90354753 8192391 0.09066917597572316 0.672699946907879 chr17 81195210 5194322 0.06397325655047878 0.5853224908537813 chr18 78077248 3529175 0.045201068049939466 1.1913070936801449 chr19 59128983 4758795 0.08048159732427666 0.8121423168516119 chr20 63025520 4075020 0.06465666606162075 0.5623921699159552 chr21 48129895 3341367 0.06942394119081291 0.5712419373284758 chr22 51304566 2142270 0.04175593260061882 0.4281381919954377 chrMT 16571 37678 2.2737312171866515 2.7606226336840387 chrX 155270560 10827107 0.0697305851154269 0.6175506297773072 chrY 59373566 487832 0.008216316331749384 0.19850719010575985