BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716181.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 = 3,308,474 number of mapped reads = 2,988,530 (90.33%) number of supplementary alignments = 12,668 (0.38%) number of secondary alignments = 0 number of mapped bases = 172,083,056 bp number of sequenced bases = 172,030,007 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 145,930 duplication rate = 3.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9743 >>>>>>> ACTG content number of A's = 41,212,371 bp (23.96%) number of C's = 36,101,244 bp (20.99%) number of T's = 54,013,165 bp (31.4%) number of G's = 40,701,954 bp (23.66%) number of N's = 1,273 bp (0%) GC percentage = 44.65% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 902,697 number of insertions = 12,668 mapped reads with insertion percentage = 0.42% number of deletions = 33,247 mapped reads with deletion percentage = 1.1% homopolymer indels = 40.57% >>>>>>> Coverage mean coverageData = 0.0556X std coverageData = 0.4069X There is a 4.61% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% 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% 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 13788908 0.05532145895837106 0.5571612149444357 chr2 243199373 14324253 0.0588992184613897 0.6402601719355973 chr3 198022430 11567147 0.05841331711766187 0.2879027023416033 chr4 191154276 10935311 0.05720672970977641 0.3329593483282624 chr5 180915260 10168933 0.05620826568195519 0.27766089351935036 chr6 171115067 9707789 0.05673252022862487 0.3377776367777889 chr7 159138663 9504571 0.05972509018754292 0.527254445852806 chr8 146364022 8601678 0.05876907372769519 0.41974652918297384 chr9 141213431 7384883 0.05229589669838133 0.3487474044625594 chr10 135534747 8324222 0.06141762303949998 0.5193771880625454 chr11 135006516 7643139 0.056613111918242524 0.3590320375688474 chr12 133851895 7917187 0.05914886001427174 0.2921953001283001 chr13 115169878 5351365 0.04646497064102126 0.2529573803279556 chr14 107349540 5182885 0.04828045839786552 0.2791844429873064 chr15 102531392 5054804 0.049300062170227824 0.2678318035745442 chr16 90354753 5223085 0.05780642220337872 0.320535179745744 chr17 81195210 4925039 0.0606567678068694 0.31050547139293855 chr18 78077248 4486651 0.057464256424611684 0.5549538896814235 chr19 59128983 3883231 0.06567390140973675 0.48130415553673017 chr20 63025520 3745643 0.05943057669337754 0.3006520917110549 chr21 48129895 2256720 0.046888113925866656 0.30490845974693204 chr22 51304566 2147339 0.041854734722831494 0.24417227029542782 chrMT 16571 4998 0.3016112485667733 0.7428595981582126 chrX 155270560 9422891 0.0606869132178051 0.32167412254873434 chrY 59373566 530384 0.008932998903923002 0.2720157605633243