BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525105.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 = 1,085,470 number of mapped reads = 990,375 (91.24%) number of supplementary alignments = 31,055 (2.86%) number of secondary alignments = 0 number of mapped bases = 76,265,625 bp number of sequenced bases = 76,235,380 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,153 duplication rate = 1.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6405 >>>>>>> ACTG content number of A's = 19,528,349 bp (25.62%) number of C's = 15,403,047 bp (20.2%) number of T's = 22,978,255 bp (30.14%) number of G's = 18,322,894 bp (24.03%) number of N's = 2,835 bp (0%) GC percentage = 44.24% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 571,647 number of insertions = 6,658 mapped reads with insertion percentage = 0.66% number of deletions = 17,484 mapped reads with deletion percentage = 1.74% homopolymer indels = 43.06% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.2702X There is a 2.25% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% 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 7470596 0.02997222622767307 0.4583189224063639 chr2 243199373 6233432 0.025630954237698633 0.3720846387838388 chr3 198022430 4786228 0.024170130626111397 0.16519685656548502 chr4 191154276 4642445 0.024286377982985847 0.17594243497146014 chr5 180915260 4405281 0.024349969151303212 0.16733492603171535 chr6 171115067 4199671 0.024542964413531158 0.18317343190122448 chr7 159138663 4093690 0.02572404419408752 0.35984985315210233 chr8 146364022 3776346 0.025801053758962706 0.3302307091609435 chr9 141213431 3043574 0.02155300652669504 0.2426771058267862 chr10 135534747 3489932 0.02574935267337755 0.26478788651147417 chr11 135006516 4191869 0.031049382831270157 0.31644549285182005 chr12 133851895 3364192 0.025133689739693262 0.16895897287551587 chr13 115169878 2689469 0.02335219109982907 0.16290726278900572 chr14 107349540 2211063 0.020596855841208076 0.1698164321412892 chr15 102531392 2128227 0.02075683318529412 0.15223328382339435 chr16 90354753 1788281 0.019791775646821812 0.16216697449186562 chr17 81195210 2485446 0.030610746619166327 0.2143287941380874 chr18 78077248 1971179 0.025246522520875735 0.407142417595482 chr19 59128983 1593765 0.026954040457621266 0.3348893673335339 chr20 63025520 1562259 0.02478772091051371 0.17302979328729334 chr21 48129895 978786 0.02033634189312069 0.1604081444093389 chr22 51304566 851418 0.016595365020727396 0.1360232805561013 chrMT 16571 7582 0.4575463158529962 0.7716349882516995 chrX 155270560 4112583 0.026486559976340654 0.21651938284561 chrY 59373566 188311 0.0031716302840897243 0.0880299308046416