BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472569.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 = 422,354,902 number of mapped reads = 415,525,690 (98.38%) number of supplementary alignments = 325,809 (0.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 208,563,107 number of mapped paired reads (second in pair) = 206,962,583 number of mapped paired reads (both in pair) = 413,215,876 number of mapped paired reads (singletons) = 2,309,814 number of mapped bases = 39,137,436,442 bp number of sequenced bases = 39,130,133,916 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 281,651,938 duplication rate = 54.8% >>>>>>> Insert size mean insert size = 9,077.8335 std insert size = 872,826.7174 median insert size = 155 >>>>>>> Mapping quality mean mapping quality = 51.8722 >>>>>>> ACTG content number of A's = 9,886,673,487 bp (25.27%) number of C's = 9,696,741,368 bp (24.78%) number of T's = 10,025,410,449 bp (25.62%) number of G's = 9,513,513,674 bp (24.31%) number of N's = 7,794,938 bp (0.02%) GC percentage = 49.09% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 386,981,543 number of insertions = 2,978,315 mapped reads with insertion percentage = 0.7% number of deletions = 3,150,875 mapped reads with deletion percentage = 0.74% homopolymer indels = 39.47% >>>>>>> Coverage mean coverageData = 12.6425X std coverageData = 127.7216X There is a 78.72% of reference with a coverageData >= 1X There is a 70.16% of reference with a coverageData >= 2X There is a 60.26% of reference with a coverageData >= 3X There is a 52.62% of reference with a coverageData >= 4X There is a 44.74% of reference with a coverageData >= 5X There is a 38.71% of reference with a coverageData >= 6X There is a 32.86% of reference with a coverageData >= 7X There is a 28.33% of reference with a coverageData >= 8X There is a 24.15% of reference with a coverageData >= 9X There is a 20.88% of reference with a coverageData >= 10X There is a 17.96% of reference with a coverageData >= 11X There is a 15.67% of reference with a coverageData >= 12X There is a 13.67% of reference with a coverageData >= 13X There is a 12.08% of reference with a coverageData >= 14X There is a 10.72% of reference with a coverageData >= 15X There is a 9.64% of reference with a coverageData >= 16X There is a 8.71% of reference with a coverageData >= 17X There is a 7.97% of reference with a coverageData >= 18X There is a 7.34% of reference with a coverageData >= 19X There is a 6.83% of reference with a coverageData >= 20X There is a 6.4% of reference with a coverageData >= 21X There is a 6.04% of reference with a coverageData >= 22X There is a 5.73% of reference with a coverageData >= 23X There is a 5.47% of reference with a coverageData >= 24X There is a 5.25% of reference with a coverageData >= 25X There is a 5.06% of reference with a coverageData >= 26X There is a 4.89% of reference with a coverageData >= 27X There is a 4.75% of reference with a coverageData >= 28X There is a 4.62% of reference with a coverageData >= 29X There is a 4.5% of reference with a coverageData >= 30X There is a 4.4% of reference with a coverageData >= 31X There is a 4.31% of reference with a coverageData >= 32X There is a 4.22% of reference with a coverageData >= 33X There is a 4.14% of reference with a coverageData >= 34X There is a 4.07% of reference with a coverageData >= 35X There is a 4% of reference with a coverageData >= 36X There is a 3.94% of reference with a coverageData >= 37X There is a 3.88% of reference with a coverageData >= 38X There is a 3.82% of reference with a coverageData >= 39X There is a 3.77% of reference with a coverageData >= 40X There is a 3.72% of reference with a coverageData >= 41X There is a 3.67% of reference with a coverageData >= 42X There is a 3.62% of reference with a coverageData >= 43X There is a 3.58% of reference with a coverageData >= 44X There is a 3.53% of reference with a coverageData >= 45X There is a 3.49% of reference with a coverageData >= 46X There is a 3.45% of reference with a coverageData >= 47X There is a 3.41% of reference with a coverageData >= 48X There is a 3.37% of reference with a coverageData >= 49X There is a 3.34% of reference with a coverageData >= 50X There is a 3.3% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3284589943 13.177860620054384 104.09175813170152 chr2 243199373 3014814870 12.396474681700763 91.9556239780188 chr3 198022430 1865989283 9.423120820202035 48.59159746671871 chr4 191154276 1533596597 8.022821299587354 59.22804213896452 chr5 180915260 1700197143 9.39775419165857 64.01868391890983 chr6 171115067 2041795111 11.932292969852853 55.81689868944281 chr7 159138663 3229751662 20.295204201885245 432.65179268108216 chr8 146364022 1979550501 13.524843564356273 196.1119430030141 chr9 141213431 1503027057 10.643655113797214 55.975003675089035 chr10 135534747 1464137068 10.802669429116948 75.41992564307282 chr11 135006516 1685948086 12.487901591357264 53.918315161230026 chr12 133851895 1836546369 13.720734913764202 52.48382090299853 chr13 115169878 1099279947 9.544856398996966 40.52701894394748 chr14 107349540 936408012 8.722981132476209 38.59007510371766 chr15 102531392 1360054830 13.264765097503016 66.24723704814915 chr16 90354753 1824679640 20.194617099999157 96.37191385354893 chr17 81195210 2139983845 26.356035596188494 128.18461528449336 chr18 78077248 641175861 8.212070448487118 65.08941439346374 chr19 59128983 1828509639 30.92408403168375 116.58502821731689 chr20 63025520 1205965468 19.13455800126679 84.14914041204607 chr21 48129895 547227455 11.369803632440918 75.653684393183 chr22 51304566 792527831 15.44751067575545 78.09232465335471 chrMT 16571 5562176 335.657232514634 99.84057493612661 chrX 155270560 1417199482 9.127290337588787 40.000965089710974 chrY 59373566 198918566 3.350288342121812 89.15131832982327