BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751230.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 5,247,109 number of mapped reads = 3,754,873 (71.56%) number of supplementary alignments = 211,799 (4.04%) number of secondary alignments = 0 number of mapped bases = 367,974,970 bp number of sequenced bases = 367,853,917 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,912 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.1208 >>>>>>> ACTG content number of A's = 107,861,381 bp (29.32%) number of C's = 75,964,482 bp (20.65%) number of T's = 108,777,660 bp (29.57%) number of G's = 75,247,880 bp (20.46%) number of N's = 2,514 bp (0%) GC percentage = 41.11% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 1,338,850 number of insertions = 338,002 mapped reads with insertion percentage = 8.55% number of deletions = 55,789 mapped reads with deletion percentage = 1.46% homopolymer indels = 54.52% >>>>>>> Coverage mean coverageData = 0.1189X std coverageData = 1.0743X There is a 9.32% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 44630190 0.17905748768425336 2.8297051655566685 chr2 243199373 27252262 0.11205728725295686 0.5472923539159895 chr3 198022430 24027991 0.12133974418958499 0.49563183565785635 chr4 191154276 16057291 0.0840017358544467 0.40591815117824803 chr5 180915260 26910067 0.14874404182377982 0.5006164373294909 chr6 171115067 20358717 0.11897676433133735 0.7457103381651582 chr7 159138663 19843503 0.12469316146007837 0.7108198634952966 chr8 146364022 17424091 0.11904627081100573 0.4988424988332456 chr9 141213431 15996090 0.1132759815176504 0.589464370569724 chr10 135534747 18527651 0.13670037691515372 1.8118433930803493 chr11 135006516 16899066 0.12517222502060568 0.6097638621514593 chr12 133851895 19772329 0.14771796095976078 0.4754940678954111 chr13 115169878 10096985 0.08767036290513393 0.3574897919944035 chr14 107349540 8002797 0.07454896406635743 0.3420053195002562 chr15 102531392 9231234 0.09003324562296004 0.362024513101468 chr16 90354753 11359522 0.12572135524514133 0.8947392548618484 chr17 81195210 12040045 0.14828516361987362 0.648741367780083 chr18 78077248 7643849 0.09790110686278287 1.10493739961757 chr19 59128983 7761320 0.1312608403902364 1.9764085393771957 chr20 63025520 7979478 0.12660709503071138 0.4585482273991587 chr21 48129895 4701430 0.09768211628136733 0.4066669994409987 chr22 51304566 4948461 0.09645264322087824 0.40963748222141483 chrMT 16571 769117 46.413433106028606 17.848890413537276 chrX 155270560 14938503 0.0962095003714806 0.4202098791272471 chrY 59373566 802981 0.01352421715751417 0.5459482208753926