BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174044.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 5,241,540 number of mapped reads = 5,101,194 (97.32%) number of supplementary alignments = 521,456 (9.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,555,185 number of mapped paired reads (second in pair) = 2,546,009 number of mapped paired reads (both in pair) = 5,008,674 number of mapped paired reads (singletons) = 92,520 number of mapped bases = 601,381,862 bp number of sequenced bases = 601,020,574 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,956,196 duplication rate = 64.15% >>>>>>> Insert size mean insert size = 763,229.9966 std insert size = 7,841,107.124 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 52.6511 >>>>>>> ACTG content number of A's = 182,626,922 bp (30.39%) number of C's = 115,792,490 bp (19.27%) number of T's = 182,441,892 bp (30.36%) number of G's = 120,151,875 bp (19.99%) number of N's = 7,395 bp (0%) GC percentage = 39.26% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 6,165,553 number of insertions = 64,026 mapped reads with insertion percentage = 1.21% number of deletions = 147,155 mapped reads with deletion percentage = 2.81% homopolymer indels = 42.59% >>>>>>> Coverage mean coverageData = 0.1943X std coverageData = 2.9172X There is a 4.07% of reference with a coverageData >= 1X There is a 3.17% of reference with a coverageData >= 2X There is a 2.42% of reference with a coverageData >= 3X There is a 1.99% of reference with a coverageData >= 4X There is a 1.52% of reference with a coverageData >= 5X There is a 1.24% of reference with a coverageData >= 6X There is a 0.92% of reference with a coverageData >= 7X There is a 0.76% of reference with a coverageData >= 8X There is a 0.56% of reference with a coverageData >= 9X There is a 0.47% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 55195369 0.22144526171511525 1.7065869406230263 chr2 243199373 45180031 0.18577363273054162 8.476246439192147 chr3 198022430 37673128 0.19024677153997152 1.2708142074282354 chr4 191154276 38651637 0.20220126804801375 1.610519108279436 chr5 180915260 31299940 0.1730088440300724 1.2013687652577774 chr6 171115067 30049465 0.17560969660257914 1.2677655832994115 chr7 159138663 50355825 0.31642734738823336 3.1494635990779005 chr8 146364022 60415896 0.41277832608344145 2.277957706984427 chr9 141213431 21147799 0.1497577025800046 1.4401479913169242 chr10 135534747 22806296 0.1682689974697042 3.7425898659855803 chr11 135006516 25440378 0.1884381491631115 1.296183459383879 chr12 133851895 23213685 0.17342813861544507 1.2085960622982135 chr13 115169878 15006019 0.13029465048143926 1.0504995072558068 chr14 107349540 20895436 0.1946485844280283 1.278901509372225 chr15 102531392 14370055 0.14015273488143026 1.0746754727399563 chr16 90354753 13966399 0.15457293098903163 1.571560467440428 chr17 81195210 15242338 0.18772459606915234 1.3619851379634063 chr18 78077248 10472959 0.1341358624730216 1.7747780654368666 chr19 59128983 7572217 0.1280626964275709 1.2930294328878702 chr20 63025520 24162542 0.3833771145402688 1.808294484584595 chr21 48129895 7059193 0.14666961147536267 1.2185503265196955 chr22 51304566 6148883 0.11985059965228047 0.9601892689007734 chrMT 16571 1145021 69.09788184177177 52.64147626308584 chrX 155270560 22725359 0.14635974134439908 1.1193155204545986 chrY 59373566 1185992 0.01997508453509429 0.8350822225513864