BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038449.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 18,244,120 number of mapped reads = 16,693,240 (91.5%) number of supplementary alignments = 230,653 (1.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,482,298 number of mapped paired reads (second in pair) = 8,210,942 number of mapped paired reads (both in pair) = 16,361,428 number of mapped paired reads (singletons) = 331,812 number of mapped bases = 2,244,344,196 bp number of sequenced bases = 2,242,838,224 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,297,967 duplication rate = 14.12% >>>>>>> Insert size mean insert size = 77,783.8701 std insert size = 2,722,916.6737 median insert size = 249 >>>>>>> Mapping quality mean mapping quality = 53.3523 >>>>>>> ACTG content number of A's = 640,989,769 bp (28.58%) number of C's = 445,337,822 bp (19.86%) number of T's = 653,158,158 bp (29.12%) number of G's = 503,176,755 bp (22.43%) number of N's = 175,720 bp (0.01%) GC percentage = 42.29% >>>>>>> Mismatches and indels general error rate = 0.0132 number of mismatches = 28,534,818 number of insertions = 377,987 mapped reads with insertion percentage = 2.15% number of deletions = 772,355 mapped reads with deletion percentage = 4.46% homopolymer indels = 47.25% >>>>>>> Coverage mean coverageData = 0.725X std coverageData = 9.3934X There is a 26.74% of reference with a coverageData >= 1X There is a 15.64% of reference with a coverageData >= 2X There is a 9.08% of reference with a coverageData >= 3X There is a 5.73% of reference with a coverageData >= 4X There is a 3.62% of reference with a coverageData >= 5X There is a 2.37% of reference with a coverageData >= 6X There is a 1.57% of reference with a coverageData >= 7X There is a 1.07% of reference with a coverageData >= 8X There is a 0.74% of reference with a coverageData >= 9X There is a 0.52% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% 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 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 202652437 0.8130468689985731 12.826373335580485 chr2 243199373 203380640 0.836271234959146 11.178558441186645 chr3 198022430 167079686 0.843741216588444 1.9287169367830599 chr4 191154276 97218160 0.5085848040354588 7.983554779415344 chr5 180915260 154610326 0.8546008003968266 1.8296953838563668 chr6 171115067 131774811 0.7700947281281783 7.34971717464113 chr7 159138663 108116561 0.6793858824866462 9.89747356617901 chr8 146364022 142845175 0.9759582515435384 3.8705097866672182 chr9 141213431 94803793 0.6713511054058307 15.39601826794365 chr10 135534747 118102193 0.8713794478105308 24.13613696080107 chr11 135006516 102166974 0.7567558739164856 7.550690895066343 chr12 133851895 92849895 0.6936763577385289 1.7735887442668243 chr13 115169878 76099124 0.6607554450999765 1.5623022860017377 chr14 107349540 72703040 0.6772552541911219 1.6701100388070882 chr15 102531392 60642815 0.5914560781540935 1.5039864350911527 chr16 90354753 69682830 0.7712137733363069 10.115000288372896 chr17 81195210 54298354 0.6687383898631458 12.34748159972328 chr18 78077248 89904167 1.1514771499118412 10.813506208170732 chr19 59128983 27844971 0.4709191598982854 5.45465362303084 chr20 63025520 59167330 0.9387836863543529 3.0600549303458764 chr21 48129895 21725980 0.451403020929092 3.8100111474643503 chr22 51304566 12172835 0.23726611389715294 0.9315709592774206 chrMT 16571 4046570 244.19588437632007 130.4220378176672 chrX 155270560 76009984 0.4895324908984678 2.191482114194513 chrY 59373566 4445545 0.07487414517093348 8.08508418336217