BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524987.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 = 1,897,541 number of mapped reads = 1,728,375 (91.08%) number of supplementary alignments = 4,130 (0.22%) number of secondary alignments = 0 number of mapped bases = 101,458,387 bp number of sequenced bases = 101,425,302 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,162 duplication rate = 2.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8776 >>>>>>> ACTG content number of A's = 25,511,692 bp (25.15%) number of C's = 19,738,914 bp (19.46%) number of T's = 31,495,023 bp (31.05%) number of G's = 24,678,448 bp (24.33%) number of N's = 1,225 bp (0%) GC percentage = 43.79% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 480,928 number of insertions = 5,670 mapped reads with insertion percentage = 0.33% number of deletions = 19,368 mapped reads with deletion percentage = 1.11% homopolymer indels = 44.66% >>>>>>> Coverage mean coverageData = 0.0328X std coverageData = 0.2812X There is a 2.91% of reference with a coverageData >= 1X There is a 0.26% 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 0.01% 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 8152327 0.03270734880134963 0.508688193026124 chr2 243199373 8464052 0.03480293512105395 0.31056894643169813 chr3 198022430 6812346 0.034401890735307104 0.2055327798689063 chr4 191154276 6933018 0.036269227898412276 0.23479826833608697 chr5 180915260 6167947 0.034093016807979604 0.2048815338937861 chr6 171115067 5824214 0.03403682739404824 0.2546564287426763 chr7 159138663 5525823 0.034723321761224044 0.3074449489518624 chr8 146364022 5152956 0.035206438915705664 0.29639331825907445 chr9 141213431 4210956 0.029819798089885656 0.23493775460044017 chr10 135534747 4910498 0.036230546842722186 0.2952279657126935 chr11 135006516 4689463 0.03473508641612528 0.28900069888755714 chr12 133851895 4559132 0.03406101945736368 0.2058965398213196 chr13 115169878 3164625 0.02747788792482701 0.18323034843301997 chr14 107349540 3144965 0.029296492560657455 0.1951599436921207 chr15 102531392 2897192 0.02825663383171468 0.19673549090352224 chr16 90354753 2907738 0.032181350769671185 0.20789432119542084 chr17 81195210 2655403 0.032703936599215645 0.22163054540422478 chr18 78077248 2740679 0.03510214653057444 0.4044431791352303 chr19 59128983 1939912 0.032808140806345344 0.3305499000474451 chr20 63025520 2104741 0.033395059652026673 0.205396392374231 chr21 48129895 1333388 0.027703945749310278 0.20522531524031312 chr22 51304566 1206832 0.02352289657805506 0.1690814024595617 chrMT 16571 11021 0.6650775451089252 1.0636468161664616 chrX 155270560 5650365 0.036390446456817056 0.23255356477415576 chrY 59373566 298794 0.005032441541409185 0.13861896654947367