BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173927.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 = 10,496,860 number of mapped reads = 10,269,908 (97.84%) number of supplementary alignments = 1,427,944 (13.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,138,776 number of mapped paired reads (second in pair) = 5,131,132 number of mapped paired reads (both in pair) = 10,128,322 number of mapped paired reads (singletons) = 141,586 number of mapped bases = 1,162,494,573 bp number of sequenced bases = 1,161,581,148 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,504,710 duplication rate = 66.96% >>>>>>> Insert size mean insert size = 1,091,792.9982 std insert size = 9,867,821.1827 median insert size = 152 >>>>>>> Mapping quality mean mapping quality = 52.4764 >>>>>>> ACTG content number of A's = 345,013,150 bp (29.7%) number of C's = 231,907,217 bp (19.96%) number of T's = 342,988,389 bp (29.53%) number of G's = 241,663,236 bp (20.8%) number of N's = 9,156 bp (0%) GC percentage = 40.77% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 10,076,795 number of insertions = 131,148 mapped reads with insertion percentage = 1.23% number of deletions = 408,506 mapped reads with deletion percentage = 3.88% homopolymer indels = 40.03% >>>>>>> Coverage mean coverageData = 0.3755X std coverageData = 6.6499X There is a 7.39% of reference with a coverageData >= 1X There is a 5.71% of reference with a coverageData >= 2X There is a 4.38% of reference with a coverageData >= 3X There is a 3.57% of reference with a coverageData >= 4X There is a 2.74% of reference with a coverageData >= 5X There is a 2.29% of reference with a coverageData >= 6X There is a 1.75% of reference with a coverageData >= 7X There is a 1.52% of reference with a coverageData >= 8X There is a 1.16% of reference with a coverageData >= 9X There is a 1.04% of reference with a coverageData >= 10X There is a 0.8% of reference with a coverageData >= 11X There is a 0.73% of reference with a coverageData >= 12X There is a 0.56% of reference with a coverageData >= 13X There is a 0.51% of reference with a coverageData >= 14X There is a 0.39% of reference with a coverageData >= 15X There is a 0.36% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.19% of reference with a coverageData >= 19X There is a 0.18% of reference with a coverageData >= 20X There is a 0.14% of reference with a coverageData >= 21X There is a 0.13% of reference with a coverageData >= 22X There is a 0.1% of reference with a coverageData >= 23X There is a 0.09% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% 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% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 97126985 0.38967600004495073 3.12121001254076 chr2 243199373 108516098 0.446202211220339 21.859483601430252 chr3 198022430 60275114 0.30438528605067616 1.7343985526680912 chr4 191154276 86663863 0.4533713020366858 2.8398969058273753 chr5 180915260 62249717 0.3440821796900936 1.8392929541567202 chr6 171115067 68291233 0.3990953818228058 2.7360548741417 chr7 159138663 61340568 0.38545358396029755 3.233953662092329 chr8 146364022 61224472 0.4183027438259383 4.105278000202724 chr9 141213431 50919819 0.3605876483519475 3.0980776794087763 chr10 135534747 66992966 0.4942862806981888 3.9639556055713903 chr11 135006516 54031303 0.4002125571479824 2.2688303323229038 chr12 133851895 56636687 0.42312951191314846 2.175376319307822 chr13 115169878 40976003 0.3557875002698188 1.8768314673501127 chr14 107349540 38833744 0.3617504462524944 1.9407368597304708 chr15 102531392 35662526 0.3478205582149904 1.9356498369467785 chr16 90354753 30401532 0.33646854194820275 2.2471889078797376 chr17 81195210 34782304 0.4283787676637575 2.3724228253502715 chr18 78077248 31481916 0.4032149801181517 3.860899006038335 chr19 59128983 23373716 0.395300490793153 2.5227226981426853 chr20 63025520 26594813 0.4219689579713107 2.1514559843860583 chr21 48129895 18145989 0.3770211632499925 2.695304375599513 chr22 51304566 14726976 0.2870500064263286 2.159089311356645 chrMT 16571 839959 50.688491943757164 40.063898633725145 chrX 155270560 22295850 0.1435935440691397 1.2365962583155212 chrY 59373566 10110420 0.1702848705432313 2.6972705939470103