BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472598.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 8,254,052 number of mapped reads = 6,777,787 (82.11%) number of supplementary alignments = 124,548 (1.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,431,350 number of mapped paired reads (second in pair) = 3,346,437 number of mapped paired reads (both in pair) = 6,598,148 number of mapped paired reads (singletons) = 179,639 number of mapped bases = 555,126,860 bp number of sequenced bases = 554,865,336 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,527,801 duplication rate = 17.92% >>>>>>> Insert size mean insert size = 72,702.6508 std insert size = 2,578,802.7415 median insert size = 130 >>>>>>> Mapping quality mean mapping quality = 51.6969 >>>>>>> ACTG content number of A's = 147,617,301 bp (26.6%) number of C's = 107,360,489 bp (19.35%) number of T's = 169,080,147 bp (30.47%) number of G's = 130,452,435 bp (23.51%) number of N's = 354,964 bp (0.06%) GC percentage = 42.86% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 6,315,022 number of insertions = 45,122 mapped reads with insertion percentage = 0.66% number of deletions = 141,645 mapped reads with deletion percentage = 2.04% homopolymer indels = 43.3% >>>>>>> Coverage mean coverageData = 0.1793X std coverageData = 3.6039X There is a 8.06% of reference with a coverageData >= 1X There is a 4.37% of reference with a coverageData >= 2X There is a 2.05% of reference with a coverageData >= 3X There is a 1.16% of reference with a coverageData >= 4X There is a 0.64% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% 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% 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 30937604 0.1241224751050871 2.004927342002826 chr2 243199373 52105171 0.2142487883798944 2.0472072406727673 chr3 198022430 29887049 0.15092759441443074 0.7046387149291092 chr4 191154276 30189164 0.15793088510350667 1.0040805435859341 chr5 180915260 24888361 0.13756916359626048 0.6771617107377712 chr6 171115067 36188118 0.21148411203322032 1.5527911582880325 chr7 159138663 51322122 0.32249939161547436 3.039825998994376 chr8 146364022 27451656 0.18755740396365986 1.912971011457592 chr9 141213431 19446152 0.1377075244351226 1.6101452298284369 chr10 135534747 29039724 0.21426036232612733 1.6094224984439967 chr11 135006516 26536990 0.19656080896125044 1.564300209623303 chr12 133851895 24796806 0.1852555468116458 0.8018657647285844 chr13 115169878 28034020 0.24341451503491215 0.9144455394334808 chr14 107349540 17681652 0.164711017858111 17.29012477786179 chr15 102531392 13957749 0.13613146888710922 0.675335842143637 chr16 90354753 14792861 0.16371978793412229 0.8863152130713616 chr17 81195210 12042512 0.1483155471856037 1.1340739427118303 chr18 78077248 12197190 0.1562195173682351 2.3507848339106006 chr19 59128983 6604153 0.11169062386883942 1.3951368722021598 chr20 63025520 17103986 0.2713819100580209 3.920067614011544 chr21 48129895 7592528 0.15775077007751628 0.8022659420711541 chr22 51304566 3494762 0.06811795269840115 0.4759923692246184 chrMT 16571 949839 57.31935308671776 25.04335417366019 chrX 155270560 36607403 0.2357652538897264 1.083711981761801 chrY 59373566 1279288 0.021546423538043848 0.7582235422390882