BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716785.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,432,719 number of mapped reads = 3,139,951 (91.47%) number of supplementary alignments = 65,546 (1.91%) number of secondary alignments = 0 number of mapped bases = 231,572,640 bp number of sequenced bases = 231,494,786 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,555 duplication rate = 3.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4102 >>>>>>> ACTG content number of A's = 60,005,818 bp (25.92%) number of C's = 47,268,499 bp (20.42%) number of T's = 69,218,555 bp (29.9%) number of G's = 54,974,874 bp (23.75%) number of N's = 27,040 bp (0.01%) GC percentage = 44.17% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 1,617,038 number of insertions = 16,722 mapped reads with insertion percentage = 0.53% number of deletions = 45,560 mapped reads with deletion percentage = 1.43% homopolymer indels = 42.34% >>>>>>> Coverage mean coverageData = 0.0748X std coverageData = 0.508X There is a 5.89% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 18296548 0.07340622834396067 0.5578584535491036 chr2 243199373 19777465 0.08132202298070892 0.7193899154019769 chr3 198022430 15263373 0.07707901069590956 0.33732154920852536 chr4 191154276 14560766 0.07617285003867766 0.3738968720283469 chr5 180915260 14034064 0.07757258287664623 0.3443899021889029 chr6 171115067 13462747 0.07867657264804157 0.41128913625082497 chr7 159138663 12785665 0.08034292081491222 0.6831668071596824 chr8 146364022 11807263 0.08067052844448344 0.6858673870596323 chr9 141213431 9616293 0.06809758060477973 0.5431435731222669 chr10 135534747 11000955 0.0811670456727971 0.514920560826549 chr11 135006516 10464262 0.077509310735787 0.5413138242865154 chr12 133851895 10776216 0.08050850531477347 0.3548895830000938 chr13 115169878 7288480 0.06328460294105721 0.30515352303990223 chr14 107349540 7036549 0.06554801259511685 0.40223109524504985 chr15 102531392 6818457 0.06650116483349802 0.3220421759468236 chr16 90354753 6901576 0.076383098518348 0.38711956354362204 chr17 81195210 6434606 0.07924859114226074 0.37768013248314247 chr18 78077248 6366317 0.08153869613847045 1.0294791636161014 chr19 59128983 4754811 0.08041421919940683 0.5350802227055229 chr20 63025520 5029693 0.0798040698434539 0.36401092610059094 chr21 48129895 3107447 0.06456376021597388 0.3521283915661329 chr22 51304566 2756533 0.053728804566829394 0.285326475976511 chrMT 16571 7597 0.45845151167702614 0.9626410498360966 chrX 155270560 12661463 0.08154451816236123 0.45567892472360827 chrY 59373566 563494 0.00949065447744877 0.2580251866310342