BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714099.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 579,502 number of mapped reads = 374,646 (64.65%) number of supplementary alignments = 11,895 (2.05%) number of secondary alignments = 0 number of mapped bases = 48,108,641 bp number of sequenced bases = 47,009,146 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 320,106 duplication rate = 43.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.2209 >>>>>>> ACTG content number of A's = 12,717,306 bp (27.05%) number of C's = 9,307,706 bp (19.8%) number of T's = 12,054,807 bp (25.64%) number of G's = 12,928,879 bp (27.5%) number of N's = 448 bp (0%) GC percentage = 47.3% >>>>>>> Mismatches and indels general error rate = 0.0463 number of mismatches = 2,033,464 number of insertions = 53,036 mapped reads with insertion percentage = 13.44% number of deletions = 181,211 mapped reads with deletion percentage = 44.58% homopolymer indels = 30.39% >>>>>>> Coverage mean coverageData = 0.0155X std coverageData = 4.8954X There is a 0.05% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% 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 0.02% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2823057 0.01132617840097578 1.5857079784822288 chr2 243199373 6638904 0.02729819537815996 14.73230946900063 chr3 198022430 2797797 0.014128687341125953 2.977965323269255 chr4 191154276 1960930 0.010258363250006503 1.539710631706434 chr5 180915260 2372945 0.013116334133450102 1.7353902303176674 chr6 171115067 2168445 0.01267243754753636 2.4137968085109884 chr7 159138663 2481692 0.015594525888407143 2.8088922483259875 chr8 146364022 2778428 0.01898299843113084 6.113339373939021 chr9 141213431 1538295 0.010893404324975292 1.928395922401651 chr10 135534747 2246505 0.016575122245220262 2.430678205926368 chr11 135006516 2382617 0.017648162996814168 3.1858787799943284 chr12 133851895 2279228 0.017027984549639736 2.310708118591712 chr13 115169878 1257430 0.010918045775823431 1.9362138606175505 chr14 107349540 1226248 0.011422946013555344 1.6614050430797314 chr15 102531392 1474306 0.014379069387841725 2.1496801597400164 chr16 90354753 1008120 0.011157354389536099 1.5549716100142 chr17 81195210 1256367 0.015473412778906539 2.470594400667397 chr18 78077248 998010 0.012782340893982329 1.4109318676842257 chr19 59128983 900257 0.015225308373729344 2.1562327607288716 chr20 63025520 936942 0.014866073298562233 2.1979822933218225 chr21 48129895 441264 0.009168189542071513 1.7119408365606552 chr22 51304566 287213 0.005598195684961062 0.7445601530635142 chrMT 16571 218379 13.178383923722166 95.22559064365691 chrX 155270560 5483571 0.035316231228894907 4.996248015034503 chrY 59373566 151691 0.0025548574933161334 0.8091830524389627