BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173984.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 11,574,094 number of mapped reads = 11,307,775 (97.7%) number of supplementary alignments = 1,519,598 (13.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,656,701 number of mapped paired reads (second in pair) = 5,651,074 number of mapped paired reads (both in pair) = 11,137,604 number of mapped paired reads (singletons) = 170,171 number of mapped bases = 1,278,929,153 bp number of sequenced bases = 1,278,073,981 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,101,350 duplication rate = 65.58% >>>>>>> Insert size mean insert size = 951,834.6165 std insert size = 9,331,725.7702 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 52.5167 >>>>>>> ACTG content number of A's = 381,145,095 bp (29.82%) number of C's = 254,260,759 bp (19.89%) number of T's = 378,120,012 bp (29.59%) number of G's = 264,538,676 bp (20.7%) number of N's = 9,439 bp (0%) GC percentage = 40.59% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 10,912,835 number of insertions = 139,686 mapped reads with insertion percentage = 1.19% number of deletions = 357,542 mapped reads with deletion percentage = 3.08% homopolymer indels = 41.09% >>>>>>> Coverage mean coverageData = 0.4131X std coverageData = 6.9317X There is a 8.65% of reference with a coverageData >= 1X There is a 6.6% of reference with a coverageData >= 2X There is a 5% of reference with a coverageData >= 3X There is a 4.03% of reference with a coverageData >= 4X There is a 3.04% of reference with a coverageData >= 5X There is a 2.5% of reference with a coverageData >= 6X There is a 1.87% of reference with a coverageData >= 7X There is a 1.6% of reference with a coverageData >= 8X There is a 1.21% of reference with a coverageData >= 9X There is a 1.07% of reference with a coverageData >= 10X There is a 0.8% of reference with a coverageData >= 11X There is a 0.73% of reference with a coverageData >= 12X There is a 0.54% of reference with a coverageData >= 13X There is a 0.5% of reference with a coverageData >= 14X There is a 0.37% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.12% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% 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% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 104453657 0.41907079942641345 3.6084802454957408 chr2 243199373 117314404 0.48237954955582885 22.725803410000207 chr3 198022430 87708523 0.44292216290851494 1.9857499642004535 chr4 191154276 82902280 0.43369304487857757 3.0659238855635933 chr5 180915260 77389500 0.4277665687239429 1.9575633977213378 chr6 171115067 75399840 0.44063822854360335 2.500788377855664 chr7 159138663 71971924 0.45225919737681847 3.3950300509532525 chr8 146364022 67102786 0.45846503179586034 4.057512808563982 chr9 141213431 55480139 0.3928814604044285 3.209932387467035 chr10 135534747 62915290 0.4642004459564897 3.9998002751315 chr11 135006516 57456347 0.42558202894443997 2.1238739852083297 chr12 133851895 59262043 0.442743399337006 2.0958275976216085 chr13 115169878 40906452 0.3551836010454053 1.7679376841415229 chr14 107349540 39609916 0.3689807706674849 1.8619871220680357 chr15 102531392 36953474 0.36041131676043175 1.8688176911087413 chr16 90354753 38927631 0.43083102667548656 2.609132815593084 chr17 81195210 36426541 0.4486291863768811 2.4005812663163586 chr18 78077248 35339950 0.45262801783177603 4.662020523608669 chr19 59128983 24402988 0.412707724061481 2.8519819247148543 chr20 63025520 27913734 0.44289573493403944 2.1436317899659634 chr21 48129895 17468070 0.3629359673442047 2.7285601193120677 chr22 51304566 16333232 0.3183582529477006 2.209585515542267 chrMT 16571 2507238 151.30275782994389 112.55752059446716 chrX 155270560 33788153 0.2176082381618254 1.4126782024400348 chrY 59373566 8995041 0.15149908631056452 2.3534789742966513