BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716186.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 = 3,683,682 number of mapped reads = 3,273,455 (88.86%) number of supplementary alignments = 12,162 (0.33%) number of secondary alignments = 0 number of mapped bases = 186,920,473 bp number of sequenced bases = 186,867,111 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,617 duplication rate = 2.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1917 >>>>>>> ACTG content number of A's = 46,102,511 bp (24.67%) number of C's = 38,589,271 bp (20.65%) number of T's = 56,494,553 bp (30.23%) number of G's = 45,679,432 bp (24.44%) number of N's = 1,344 bp (0%) GC percentage = 45.1% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 975,335 number of insertions = 10,810 mapped reads with insertion percentage = 0.33% number of deletions = 33,347 mapped reads with deletion percentage = 1.01% homopolymer indels = 41.09% >>>>>>> Coverage mean coverageData = 0.0604X std coverageData = 0.4249X There is a 5.06% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 15681983 0.06291652529122485 0.5456798751448098 chr2 243199373 14537870 0.0597775801009158 0.6452779507760502 chr3 198022430 10692559 0.053996706332711905 0.27495531912565324 chr4 191154276 11333354 0.059289042532326086 0.3272471668807207 chr5 180915260 10622644 0.05871613041376388 0.2794960686124359 chr6 171115067 9935910 0.05806566408322185 0.3579849399154635 chr7 159138663 10725961 0.06740009497252092 0.6684742293243361 chr8 146364022 9663634 0.06602465461081686 0.3911601522180464 chr9 141213431 6179901 0.04376284151045094 0.3096230260953512 chr10 135534747 8214649 0.06060917352802525 0.5712928539438769 chr11 135006516 6623419 0.04905999500053761 0.3532942622198013 chr12 133851895 9349024 0.06984603393175719 0.3115505219508452 chr13 115169878 5568734 0.048352347824836626 0.25481130670809427 chr14 107349540 6331589 0.058981053854539105 0.3080764020630844 chr15 102531392 6860528 0.06691148794702798 0.31381266411244874 chr16 90354753 6622661 0.07329621054910083 0.35263703754549136 chr17 81195210 8451082 0.10408350443332802 0.4131089593417059 chr18 78077248 3436839 0.044018444400089514 0.5237769024413849 chr19 59128983 5093610 0.08614404884995232 0.5401691260959706 chr20 63025520 6131085 0.09727940364474581 0.40303770860959937 chr21 48129895 2332137 0.04845506103846684 0.2961572765274095 chr22 51304566 1770633 0.03451219137103703 0.21635593039149878 chrMT 16571 84841 5.119847927101563 3.8849532889386382 chrX 155270560 10111104 0.06511926021262499 0.3338168754775892 chrY 59373566 564722 0.009511337082229489 0.25230988531212206