BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472462.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 = 10,015,584 number of mapped reads = 9,894,396 (98.79%) number of supplementary alignments = 38,108 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,964,935 number of mapped paired reads (second in pair) = 4,929,461 number of mapped paired reads (both in pair) = 9,827,892 number of mapped paired reads (singletons) = 66,504 number of mapped bases = 963,934,508 bp number of sequenced bases = 963,819,430 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,699,111 duplication rate = 45.4% >>>>>>> Insert size mean insert size = 16,382.2283 std insert size = 1,276,525.3238 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 54.8866 >>>>>>> ACTG content number of A's = 263,073,952 bp (27.29%) number of C's = 220,204,607 bp (22.85%) number of T's = 262,292,762 bp (27.21%) number of G's = 218,129,219 bp (22.63%) number of N's = 118,890 bp (0.01%) GC percentage = 45.48% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 5,842,870 number of insertions = 55,366 mapped reads with insertion percentage = 0.55% number of deletions = 48,973 mapped reads with deletion percentage = 0.49% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 0.3114X std coverageData = 10.5106X There is a 2.93% of reference with a coverageData >= 1X There is a 1.37% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.25% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.23% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.22% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.2% of reference with a coverageData >= 17X There is a 0.2% of reference with a coverageData >= 18X There is a 0.19% of reference with a coverageData >= 19X There is a 0.19% of reference with a coverageData >= 20X There is a 0.18% of reference with a coverageData >= 21X There is a 0.18% of reference with a coverageData >= 22X There is a 0.18% of reference with a coverageData >= 23X There is a 0.17% of reference with a coverageData >= 24X There is a 0.17% of reference with a coverageData >= 25X There is a 0.17% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.15% of reference with a coverageData >= 30X There is a 0.15% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.15% of reference with a coverageData >= 33X There is a 0.14% of reference with a coverageData >= 34X There is a 0.14% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 100537632 0.4033596048693496 13.434054911104658 chr2 243199373 79961037 0.3287880063736842 10.616257248963217 chr3 198022430 94246516 0.475938589381011 13.975947335457803 chr4 191154276 32598757 0.17053637345784511 5.945649377408546 chr5 180915260 29374089 0.16236379949375193 7.414139835519591 chr6 171115067 87668096 0.5123341710172138 14.684466774818457 chr7 159138663 56347133 0.35407569686569507 11.907353905011561 chr8 146364022 59710951 0.4079619443636224 11.525179837124334 chr9 141213431 51249717 0.362923814236905 10.482341845091621 chr10 135534747 28800794 0.2124974933549697 8.238809660485519 chr11 135006516 40707162 0.30151997996896684 9.904019088581755 chr12 133851895 43862165 0.3276917745542564 11.445735253366964 chr13 115169878 15755857 0.1368053632912592 6.133820727141297 chr14 107349540 27775977 0.25874332577484727 7.940472706513518 chr15 102531392 23885487 0.2329577950136481 8.784182693835103 chr16 90354753 37390988 0.41382425117138 11.346370080643926 chr17 81195210 35937937 0.44261154075468245 11.920819807627801 chr18 78077248 15664961 0.2006341335186404 7.476976638157315 chr19 59128983 26839210 0.4539095488924611 11.347562382291642 chr20 63025520 18780281 0.29797899327129707 12.263359976109896 chr21 48129895 5491757 0.11410282528145968 4.734903713771482 chr22 51304566 7921211 0.15439582901841525 4.205423230489725 chrMT 16571 3134 0.1891255808339871 0.5019592552580219 chrX 155270560 42828248 0.2758298031513508 9.540004849344966 chrY 59373566 595411 0.01002821693411509 0.5349568362328109