BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174037.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 = 3,653,110 number of mapped reads = 3,577,020 (97.92%) number of supplementary alignments = 335,063 (9.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,790,202 number of mapped paired reads (second in pair) = 1,786,818 number of mapped paired reads (both in pair) = 3,529,890 number of mapped paired reads (singletons) = 47,130 number of mapped bases = 423,823,764 bp number of sequenced bases = 423,602,824 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,633,038 duplication rate = 63.07% >>>>>>> Insert size mean insert size = 634,590.4596 std insert size = 7,271,154.5567 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 52.9597 >>>>>>> ACTG content number of A's = 128,684,417 bp (30.38%) number of C's = 82,090,271 bp (19.38%) number of T's = 128,214,518 bp (30.27%) number of G's = 84,608,393 bp (19.97%) number of N's = 5,225 bp (0%) GC percentage = 39.35% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 4,010,610 number of insertions = 41,863 mapped reads with insertion percentage = 1.14% number of deletions = 89,762 mapped reads with deletion percentage = 2.45% homopolymer indels = 43.36% >>>>>>> Coverage mean coverageData = 0.1369X std coverageData = 1.9332X There is a 3.22% of reference with a coverageData >= 1X There is a 2.44% of reference with a coverageData >= 2X There is a 1.77% of reference with a coverageData >= 3X There is a 1.42% of reference with a coverageData >= 4X There is a 1.03% of reference with a coverageData >= 5X There is a 0.83% of reference with a coverageData >= 6X There is a 0.59% of reference with a coverageData >= 7X There is a 0.49% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% 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% 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 32089018 0.12874197813934435 1.3467161628429631 chr2 243199373 37571342 0.15448782427576407 5.607955835746132 chr3 198022430 40317561 0.2036009809595812 1.2628889485648829 chr4 191154276 20219927 0.10577805227856896 0.9850292075353817 chr5 180915260 25821595 0.14272756759158955 1.0371494492451558 chr6 171115067 25633465 0.14980250102698436 1.2037397182341827 chr7 159138663 24282132 0.15258474303004543 1.307023756639141 chr8 146364022 24187010 0.16525242794981407 1.275222667424004 chr9 141213431 17276455 0.12234285986578713 1.0883073767782347 chr10 135534747 18680639 0.13782915018832773 1.7899574827048101 chr11 135006516 16140173 0.11955106670555071 0.960773921175511 chr12 133851895 18285997 0.1366136579538153 1.02385384483089 chr13 115169878 12092935 0.10500084926720162 0.9001990161284045 chr14 107349540 12772779 0.11898308087766375 0.9527680033384563 chr15 102531392 13553375 0.13218756456559178 0.9928326911967952 chr16 90354753 13670421 0.1512971984993418 1.2632873273783216 chr17 81195210 17122729 0.21088348684608366 1.3445814192340257 chr18 78077248 7855337 0.10060980889080517 1.2450847318428362 chr19 59128983 6478784 0.10957036078229182 1.0622759827438593 chr20 63025520 18484272 0.2932823402329723 1.6035038617186015 chr21 48129895 5119034 0.10635871946115819 0.8986380714236678 chr22 51304566 3256616 0.0634761436243316 0.6537977146664351 chrMT 16571 712577 43.00144831331845 37.14304826296827 chrX 155270560 11593453 0.07466613761166314 0.7491043456854146 chrY 59373566 606138 0.010208886560729736 0.3881631486172997