BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238285.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,322,638 number of mapped reads = 3,014,182 (90.72%) number of supplementary alignments = 31,036 (0.93%) number of secondary alignments = 0 number of mapped bases = 198,323,629 bp number of sequenced bases = 198,231,370 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,584 duplication rate = 2.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2669 >>>>>>> ACTG content number of A's = 55,190,004 bp (27.84%) number of C's = 39,069,005 bp (19.71%) number of T's = 58,332,013 bp (29.43%) number of G's = 45,585,740 bp (23%) number of N's = 54,608 bp (0.03%) GC percentage = 42.71% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,739,900 number of insertions = 17,707 mapped reads with insertion percentage = 0.58% number of deletions = 55,486 mapped reads with deletion percentage = 1.82% homopolymer indels = 44.59% >>>>>>> Coverage mean coverageData = 0.0641X std coverageData = 0.627X There is a 5.49% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 19503133 0.0782470788708687 1.0154563485162897 chr2 243199373 15201596 0.06250672365014691 0.8577986640488356 chr3 198022430 11809542 0.059637395622303996 0.2762864627772844 chr4 191154276 13007247 0.06804580714689322 0.3710251614209911 chr5 180915260 11538075 0.06377612922204573 0.2932350679113322 chr6 171115067 11960202 0.06989566850942472 0.40372425495991604 chr7 159138663 11200008 0.070378924824824 1.002449269253689 chr8 146364022 10075500 0.06883863850092888 0.6450973986489961 chr9 141213431 9288375 0.06577543604899735 0.7472996177150701 chr10 135534747 8477604 0.06254930331629276 0.6374316438555663 chr11 135006516 8344886 0.061810986960066434 0.4930956084957233 chr12 133851895 10998226 0.08216712957257721 0.3493621752139852 chr13 115169878 4246297 0.03686985758550513 0.21536167574625514 chr14 107349540 6559844 0.06110733217860086 0.48226029114881636 chr15 102531392 5803981 0.056606868265282106 0.28739936013742007 chr16 90354753 5530135 0.061204693902489005 0.389966483056634 chr17 81195210 4978960 0.0613208587058276 0.3486677837280013 chr18 78077248 5499338 0.070434577817087 1.375652738833963 chr19 59128983 4031176 0.0681759738705467 0.7596544421228248 chr20 63025520 4363317 0.06923095596831252 0.31682642391146737 chr21 48129895 1623125 0.033723842530718175 0.35915517202033576 chr22 51304566 2198071 0.042843574585544685 0.23122995964888 chrMT 16571 17197 1.0377768390561826 1.2290691358068435 chrX 155270560 11475596 0.07390709481565598 0.41840670855254564 chrY 59373566 592198 0.009974101942942083 0.2900717643922409