BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927057.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 23,881,674 number of mapped reads = 23,228,573 (97.27%) number of supplementary alignments = 477,066 (2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,653,899 number of mapped paired reads (second in pair) = 11,574,674 number of mapped paired reads (both in pair) = 22,869,218 number of mapped paired reads (singletons) = 359,355 number of mapped bases = 2,111,558,634 bp number of sequenced bases = 2,110,082,189 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,746,281 duplication rate = 5.79% >>>>>>> Insert size mean insert size = 221,363.1083 std insert size = 4,586,722.2546 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 52.9137 >>>>>>> ACTG content number of A's = 606,224,421 bp (28.73%) number of C's = 408,080,491 bp (19.34%) number of T's = 619,003,199 bp (29.34%) number of G's = 476,455,090 bp (22.58%) number of N's = 318,988 bp (0.02%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 21,685,161 number of insertions = 343,742 mapped reads with insertion percentage = 1.45% number of deletions = 1,006,566 mapped reads with deletion percentage = 4.22% homopolymer indels = 51.45% >>>>>>> Coverage mean coverageData = 0.6821X std coverageData = 2.8827X There is a 32.78% of reference with a coverageData >= 1X There is a 15.82% of reference with a coverageData >= 2X There is a 7.86% of reference with a coverageData >= 3X There is a 4.26% of reference with a coverageData >= 4X There is a 2.41% of reference with a coverageData >= 5X There is a 1.42% of reference with a coverageData >= 6X There is a 0.86% of reference with a coverageData >= 7X There is a 0.54% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% 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 175668704 0.7047874275908023 4.569027127665726 chr2 243199373 182570420 0.7507026755369143 4.264036973660425 chr3 198022430 139722481 0.7055891648233991 1.392730662819548 chr4 191154276 137969352 0.7217696349099719 2.378709511515137 chr5 180915260 122223157 0.6755823527545437 1.3266606238283107 chr6 171115067 128535484 0.7511640339655187 1.5340168353400863 chr7 159138663 106494184 0.6691911443292696 2.1686140334816093 chr8 146364022 105392019 0.7200677978089451 1.7800666858827412 chr9 141213431 85795383 0.6075582357318405 3.782047065274971 chr10 135534747 106781472 0.7878531104647283 5.668562536191297 chr11 135006516 103644532 0.7677002197434678 2.346651399327975 chr12 133851895 99692469 0.7447968443031755 1.440065474661509 chr13 115169878 64016708 0.5558459304784538 1.2092668161311173 chr14 107349540 64661427 0.602344704970324 1.3611903609727851 chr15 102531392 58655235 0.5720709907069241 1.2614008774815078 chr16 90354753 67103417 0.7426661550389053 3.7981912444633714 chr17 81195210 54496654 0.6711806521591607 2.360013310322138 chr18 78077248 59933175 0.767613825220889 3.900276396353665 chr19 59128983 31817419 0.5381019152654799 2.537359873391231 chr20 63025520 46719313 0.7412761211648868 1.5449771613500762 chr21 48129895 27638446 0.5742469623089765 1.9737847694952944 chr22 51304566 25169760 0.4905949306734219 1.2435838653409248 chrMT 16571 319709 19.293283446985697 10.825931657386354 chrX 155270560 110872355 0.7140590914336884 1.6543814004172057 chrY 59373566 5665359 0.09541887714812346 3.0857882553943456