BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716443.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 = 905,686 number of mapped reads = 818,759 (90.4%) number of supplementary alignments = 4,391 (0.48%) number of secondary alignments = 0 number of mapped bases = 47,368,677 bp number of sequenced bases = 47,354,657 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,675 duplication rate = 1.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2895 >>>>>>> ACTG content number of A's = 11,400,569 bp (24.07%) number of C's = 9,118,584 bp (19.26%) number of T's = 14,917,793 bp (31.5%) number of G's = 11,917,218 bp (25.17%) number of N's = 493 bp (0%) GC percentage = 44.42% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 239,956 number of insertions = 3,143 mapped reads with insertion percentage = 0.38% number of deletions = 8,995 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.3% >>>>>>> Coverage mean coverageData = 0.0153X std coverageData = 0.1764X There is a 1.43% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4022636 0.016138920672939868 0.24751121006057564 chr2 243199373 4409706 0.018132061549352763 0.20560956690443172 chr3 198022430 3555314 0.01795409742219606 0.14608763434216412 chr4 191154276 2673411 0.013985619657286662 0.13230054274678668 chr5 180915260 2431745 0.01344134817593607 0.1217866949458594 chr6 171115067 2677306 0.015646231783902467 0.13748519760275432 chr7 159138663 3011134 0.018921448397489677 0.3409998357147591 chr8 146364022 3005024 0.020531165780617863 0.1872463124548155 chr9 141213431 2020053 0.0143049636687887 0.13660662009649122 chr10 135534747 2355954 0.01738265686215506 0.23498583098731723 chr11 135006516 1461216 0.010823299817617692 0.12463858785859767 chr12 133851895 2272006 0.016974029392710505 0.14526922882939372 chr13 115169878 1260782 0.010947150608251925 0.10938055753677968 chr14 107349540 1235101 0.011505414927721162 0.11405694360761146 chr15 102531392 1177455 0.011483848770920813 0.1146429305849508 chr16 90354753 1505790 0.01666531034620835 0.1389825639598985 chr17 81195210 2036721 0.025084250659614032 0.17032324163602217 chr18 78077248 1099846 0.01408663891432239 0.1828712734441684 chr19 59128983 984081 0.016642954944785706 0.21069856022194178 chr20 63025520 1115624 0.017701147090892703 0.14280237943693472 chr21 48129895 511004 0.01061718501567477 0.11233383633647138 chr22 51304566 722540 0.014083346889631617 0.12449455226294458 chrMT 16571 12059 0.7277170961317965 0.9548340708345928 chrX 155270560 1696788 0.010927944099641297 0.11862738837916094 chrY 59373566 115381 0.0019433058812738315 0.06400947001190006