BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438287.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 641,799,970 number of mapped reads = 639,680,223 (99.67%) number of supplementary alignments = 10,946,375 (1.71%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 320,051,743 number of mapped paired reads (second in pair) = 319,628,480 number of mapped paired reads (both in pair) = 638,144,158 number of mapped paired reads (singletons) = 1,536,065 number of mapped bases = 92,472,066,008 bp number of sequenced bases = 92,445,322,239 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 275,116,471 duplication rate = 40.63% >>>>>>> Insert size mean insert size = 42,647.3478 std insert size = 2,011,314.5402 median insert size = 259 >>>>>>> Mapping quality mean mapping quality = 55.0195 >>>>>>> ACTG content number of A's = 28,004,404,746 bp (30.29%) number of C's = 18,429,285,440 bp (19.94%) number of T's = 26,660,608,658 bp (28.84%) number of G's = 19,350,331,906 bp (20.93%) number of N's = 691,489 bp (0%) GC percentage = 40.87% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 472,355,783 number of insertions = 11,876,525 mapped reads with insertion percentage = 1.83% number of deletions = 10,610,696 mapped reads with deletion percentage = 1.63% homopolymer indels = 48.55% >>>>>>> Coverage mean coverageData = 29.8712X std coverageData = 75.4997X There is a 91.47% of reference with a coverageData >= 1X There is a 90.78% of reference with a coverageData >= 2X There is a 89.98% of reference with a coverageData >= 3X There is a 89.1% of reference with a coverageData >= 4X There is a 88.08% of reference with a coverageData >= 5X There is a 86.96% of reference with a coverageData >= 6X There is a 85.7% of reference with a coverageData >= 7X There is a 84.33% of reference with a coverageData >= 8X There is a 82.85% of reference with a coverageData >= 9X There is a 81.26% of reference with a coverageData >= 10X There is a 79.56% of reference with a coverageData >= 11X There is a 77.78% of reference with a coverageData >= 12X There is a 75.92% of reference with a coverageData >= 13X There is a 73.99% of reference with a coverageData >= 14X There is a 72.01% of reference with a coverageData >= 15X There is a 69.98% of reference with a coverageData >= 16X There is a 67.92% of reference with a coverageData >= 17X There is a 65.83% of reference with a coverageData >= 18X There is a 63.73% of reference with a coverageData >= 19X There is a 61.62% of reference with a coverageData >= 20X There is a 59.52% of reference with a coverageData >= 21X There is a 57.43% of reference with a coverageData >= 22X There is a 55.36% of reference with a coverageData >= 23X There is a 53.31% of reference with a coverageData >= 24X There is a 51.3% of reference with a coverageData >= 25X There is a 49.32% of reference with a coverageData >= 26X There is a 47.38% of reference with a coverageData >= 27X There is a 45.48% of reference with a coverageData >= 28X There is a 43.63% of reference with a coverageData >= 29X There is a 41.83% of reference with a coverageData >= 30X There is a 40.08% of reference with a coverageData >= 31X There is a 38.39% of reference with a coverageData >= 32X There is a 36.74% of reference with a coverageData >= 33X There is a 35.15% of reference with a coverageData >= 34X There is a 33.62% of reference with a coverageData >= 35X There is a 32.14% of reference with a coverageData >= 36X There is a 30.71% of reference with a coverageData >= 37X There is a 29.33% of reference with a coverageData >= 38X There is a 28.01% of reference with a coverageData >= 39X There is a 26.74% of reference with a coverageData >= 40X There is a 25.52% of reference with a coverageData >= 41X There is a 24.35% of reference with a coverageData >= 42X There is a 23.23% of reference with a coverageData >= 43X There is a 22.16% of reference with a coverageData >= 44X There is a 21.13% of reference with a coverageData >= 45X There is a 20.14% of reference with a coverageData >= 46X There is a 19.2% of reference with a coverageData >= 47X There is a 18.3% of reference with a coverageData >= 48X There is a 17.44% of reference with a coverageData >= 49X There is a 16.62% of reference with a coverageData >= 50X There is a 15.84% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7597724332 30.48226841529113 28.991173022030274 chr2 243199373 8031816740 33.02564739753667 112.35459044693295 chr3 198022430 6685349150 33.76056515415956 130.74816841131985 chr4 191154276 6239930135 32.643424283116744 23.736199130466403 chr5 180915260 5915207686 32.69601296209065 25.936068547152672 chr6 171115067 5603417133 32.74648592458547 25.33197797248288 chr7 159138663 5106331162 32.087307168089005 25.11674052630243 chr8 146364022 4712024258 32.193869733915896 24.243904310279056 chr9 141213431 3957282520 28.023414571663512 30.72981069315209 chr10 135534747 4481017440 33.06176120283015 37.34138963015629 chr11 135006516 4427529040 32.79492850552487 24.902359093651995 chr12 133851895 4320836923 32.28073030269762 23.686563080442657 chr13 115169878 3043391285 26.42523668384888 23.19916014125637 chr14 107349540 2966702141 27.63590920836736 27.540882166602845 chr15 102531392 2721188398 26.540051245963774 26.50513099678834 chr16 90354753 2553221544 28.257744714326208 40.15502946653519 chr17 81195210 2312879897 28.485422933200123 30.140579095847592 chr18 78077248 2556854908 32.74775909109911 25.852062448369963 chr19 59128983 1466871555 24.8079956829293 151.46698651189385 chr20 63025520 2023625825 32.108038537405164 27.00771156093697 chr21 48129895 1217507247 25.29627889277548 61.52965510984571 chr22 51304566 1020914971 19.899105490922583 25.72878564716528 chrMT 16571 332220374 20048.299680164142 7829.235437167346 chrX 155270560 2728567763 17.572988485389633 25.563586905867787 chrY 59373566 449653581 7.5732958502105125 23.17824642483172