BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004095.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 = 2,532,792 number of mapped reads = 1,864,227 (73.6%) number of supplementary alignments = 16,034 (0.63%) number of secondary alignments = 0 number of mapped bases = 121,699,007 bp number of sequenced bases = 121,642,184 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 164,164 duplication rate = 7.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7263 >>>>>>> ACTG content number of A's = 32,368,164 bp (26.61%) number of C's = 22,215,335 bp (18.26%) number of T's = 39,654,141 bp (32.6%) number of G's = 27,389,040 bp (22.52%) number of N's = 15,504 bp (0.01%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 1,213,771 number of insertions = 10,065 mapped reads with insertion percentage = 0.54% number of deletions = 34,308 mapped reads with deletion percentage = 1.82% homopolymer indels = 47.55% >>>>>>> Coverage mean coverageData = 0.0393X std coverageData = 0.3557X There is a 2.6% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 14879805 0.05969816620838028 0.5618904006615081 chr2 243199373 8899498 0.036593424934528926 0.4104746128392074 chr3 198022430 8588548 0.04337159179391951 0.3004506588324304 chr4 191154276 6630445 0.034686354596640046 0.27105209554325516 chr5 180915260 6653796 0.03677852271831575 0.27356108126860723 chr6 171115067 9673624 0.05653285926013751 0.39019185773724435 chr7 159138663 5936830 0.03730601909103635 0.4077795858736701 chr8 146364022 6736055 0.04602261476525973 0.4120414779562468 chr9 141213431 4318249 0.030579591257151737 0.2983658343326148 chr10 135534747 5095183 0.03759318634357284 0.39363136701714624 chr11 135006516 4890957 0.036227562527426455 0.31737710758704507 chr12 133851895 4379834 0.03272149415591016 0.25589311867940384 chr13 115169878 3318323 0.028812420900541372 0.2398579399076829 chr14 107349540 3242399 0.03020412570002629 0.2514404521310217 chr15 102531392 2674942 0.026089005014191168 0.22994701593362496 chr16 90354753 3962187 0.04385145073663142 0.31089800766118636 chr17 81195210 2964329 0.03650866843007118 0.2817175056721246 chr18 78077248 2729481 0.03495872446733778 0.4850294181776979 chr19 59128983 1789241 0.030259965743026564 0.36586514980958385 chr20 63025520 2177991 0.03455728727029939 0.26934846862482803 chr21 48129895 1448326 0.030092024925464724 0.2608962002741333 chr22 51304566 1592681 0.031043650188951992 0.25611945067960207 chrMT 16571 78428 4.732846539134632 3.694581432807276 chrX 155270560 8689493 0.05596355806277765 0.35771309592379175 chrY 59373566 348362 0.005867291178030304 0.12566772492825715