BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867853.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 = 2,269,208 number of mapped reads = 2,089,262 (92.07%) number of supplementary alignments = 9,726 (0.43%) number of secondary alignments = 0 number of mapped bases = 123,444,553 bp number of sequenced bases = 123,406,735 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,940 duplication rate = 3.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.845 >>>>>>> ACTG content number of A's = 30,057,051 bp (24.36%) number of C's = 22,106,081 bp (17.91%) number of T's = 40,489,830 bp (32.81%) number of G's = 30,737,461 bp (24.91%) number of N's = 16,312 bp (0.01%) GC percentage = 42.82% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 620,080 number of insertions = 9,082 mapped reads with insertion percentage = 0.43% number of deletions = 23,625 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.87% >>>>>>> Coverage mean coverageData = 0.0399X std coverageData = 0.3708X There is a 3.51% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% 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 9933973 0.039855359076517605 0.7115399641650775 chr2 243199373 10641553 0.04375649850051217 0.4971749757751685 chr3 198022430 8099684 0.04090286135767549 0.2251684592282828 chr4 191154276 8052483 0.042125570866120725 0.2671329613827157 chr5 180915260 7522499 0.041580234856915886 0.22830230517758549 chr6 171115067 7259513 0.04242474451416952 0.2620362622683611 chr7 159138663 6814245 0.04281954411040892 0.43210490941093854 chr8 146364022 6215083 0.042463188118730434 0.3949746389817341 chr9 141213431 5180475 0.03668542689823888 0.30276945030692726 chr10 135534747 5884068 0.04341372327201083 0.3763928540219468 chr11 135006516 5444218 0.04032559435871969 0.3036343110302189 chr12 133851895 5568294 0.041600412157033716 0.22986926789595222 chr13 115169878 3887908 0.03375802829277982 0.20294668892362547 chr14 107349540 3650620 0.034006852754096574 0.21190014180309097 chr15 102531392 3577349 0.03489028023729552 0.20741361219819648 chr16 90354753 3588125 0.039711524638886456 0.2436435253747033 chr17 81195210 3404830 0.041933877626525014 0.2436404649957833 chr18 78077248 3314832 0.04245579967162777 0.5776748044239284 chr19 59128983 2596693 0.043915739257683495 0.5259799020157941 chr20 63025520 2530804 0.0401552260100353 0.23061936917807285 chr21 48129895 1601087 0.033265956636722355 0.2492858705274406 chr22 51304566 1466399 0.028582231842678486 0.18690990370058833 chrMT 16571 26197 1.5808943334741417 1.580972730926305 chrX 155270560 6751440 0.043481777872122054 0.26223033159977405 chrY 59373566 432181 0.0072790136944107416 0.2814822252589122