BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708534.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 25,194,632 number of mapped reads = 24,622,441 (97.73%) number of supplementary alignments = 596 (0%) number of secondary alignments = 0 number of mapped bases = 1,228,361,311 bp number of sequenced bases = 1,228,253,738 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 282,820 duplication rate = 1.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6534 >>>>>>> ACTG content number of A's = 379,172,801 bp (30.87%) number of C's = 233,344,642 bp (19%) number of T's = 379,085,872 bp (30.86%) number of G's = 236,607,344 bp (19.26%) number of N's = 43,079 bp (0%) GC percentage = 38.26% >>>>>>> Mismatches and indels general error rate = 0.002 number of mismatches = 2,306,568 number of insertions = 70,620 mapped reads with insertion percentage = 0.29% number of deletions = 64,531 mapped reads with deletion percentage = 0.26% homopolymer indels = 49.34% >>>>>>> Coverage mean coverageData = 0.3968X std coverageData = 0.7361X There is a 28.76% of reference with a coverageData >= 1X There is a 7.99% of reference with a coverageData >= 2X There is a 2.13% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% 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 97760044 0.3922158492836814 0.7532591610016396 chr2 243199373 111293753 0.457623519448794 0.7744315752398042 chr3 198022430 94245932 0.47593564022015084 0.7880506741172226 chr4 191154276 100270700 0.5245537902589216 0.8253099087354243 chr5 180915260 87782539 0.4852135690488464 0.7959743840969893 chr6 171115067 80653131 0.4713385700862917 0.7869584643982797 chr7 159138663 69541384 0.4369861018626253 0.7693055730597074 chr8 146364022 66816995 0.45651242762377764 0.773972628885163 chr9 141213431 52126261 0.3691310424997747 0.7182515354145932 chr10 135534747 53513243 0.3948304341468981 0.7169655040672304 chr11 135006516 57429414 0.4253825348696503 0.7722273693124532 chr12 133851895 57788874 0.4317374363657683 0.7663165575407622 chr13 115169878 47242301 0.41019667486319644 0.7476235857920472 chr14 107349540 39400710 0.36703194070510226 0.7203182118451172 chr15 102531392 33497024 0.3267001778343163 0.6860405397865931 chr16 90354753 21655469 0.23967160864243633 0.5674532792047471 chr17 81195210 20211475 0.2489244747319454 0.5798787576707793 chr18 78077248 35785067 0.45832900001803345 0.7698599708846451 chr19 59128983 9732493 0.16459767285359872 0.4581124804144839 chr20 63025520 19755605 0.31345405797524556 0.6535435254243274 chr21 48129895 14587829 0.30309289060364664 0.6710757596523081 chr22 51304566 6633122 0.12928911629424952 0.41333190695818617 chrMT 16571 1638 0.09884738398406856 0.36486907528550294 chrX 155270560 44472198 0.286417450932102 0.5955554875579271 chrY 59373566 6164110 0.10381909686879848 0.37725824887942966