BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068134.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 = 1,609,319 number of mapped reads = 1,452,891 (90.28%) number of supplementary alignments = 12,304 (0.76%) number of secondary alignments = 0 number of mapped bases = 97,527,111 bp number of sequenced bases = 97,491,759 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,813 duplication rate = 3.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.3721 >>>>>>> ACTG content number of A's = 27,719,978 bp (28.43%) number of C's = 17,082,142 bp (17.52%) number of T's = 31,930,684 bp (32.75%) number of G's = 20,683,303 bp (21.22%) number of N's = 75,652 bp (0.08%) GC percentage = 38.74% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 807,596 number of insertions = 6,987 mapped reads with insertion percentage = 0.48% number of deletions = 21,808 mapped reads with deletion percentage = 1.49% homopolymer indels = 48.15% >>>>>>> Coverage mean coverageData = 0.0315X std coverageData = 0.282X There is a 2.76% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 8053910 0.0323124972274392 0.5475848492913608 chr2 243199373 8418377 0.034615126248701306 0.2821721438545484 chr3 198022430 5569074 0.028123450459627226 0.18573872228787233 chr4 191154276 7193301 0.03763086628519887 0.21845347747833974 chr5 180915260 8052456 0.04450954551871412 0.23512283825983546 chr6 171115067 6382671 0.037300461682897856 0.24775535055384548 chr7 159138663 4778254 0.030025726683401883 0.2717212275620653 chr8 146364022 6098906 0.04166943430947805 0.4270286491318636 chr9 141213431 4397389 0.03114001953539391 0.25211933816418786 chr10 135534747 3427484 0.02528859997798203 0.23512393153062025 chr11 135006516 4227473 0.03131310343568899 0.21691986138864974 chr12 133851895 5035202 0.03761771172533643 0.21753278062895362 chr13 115169878 3448024 0.02993859210304972 0.1926195107901425 chr14 107349540 3359478 0.03129475915779425 0.20146343285329296 chr15 102531392 2517204 0.024550568863826602 0.17352775923113206 chr16 90354753 2016133 0.0223135245580274 0.17355391289967337 chr17 81195210 1885738 0.023224744415341742 0.18046771995472807 chr18 78077248 2549438 0.03265276460563774 0.3841658175631025 chr19 59128983 1286679 0.021760546769424394 0.3480924364347959 chr20 63025520 1700554 0.026981990787223967 0.18731691220253846 chr21 48129895 1331283 0.027660209938126814 0.18939298717658617 chr22 51304566 635351 0.012383907506400112 0.12187088207617557 chrMT 16571 16232 0.9795425743769235 1.0896383347011 chrX 155270560 4960788 0.03194931479605664 0.21327936914432857 chrY 59373566 185712 0.0031278565953070767 0.0741692959718116