BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617700.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 44,418,896 number of mapped reads = 43,762,570 (98.52%) number of supplementary alignments = 1,405,384 (3.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 22,065,291 number of mapped paired reads (second in pair) = 21,697,279 number of mapped paired reads (both in pair) = 43,299,270 number of mapped paired reads (singletons) = 463,300 number of mapped bases = 5,827,182,626 bp number of sequenced bases = 5,823,217,324 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,254,687 duplication rate = 22.77% >>>>>>> Insert size mean insert size = 213,414.7229 std insert size = 4,392,737.2913 median insert size = 263 >>>>>>> Mapping quality mean mapping quality = 53.2903 >>>>>>> ACTG content number of A's = 1,702,634,333 bp (29.24%) number of C's = 1,085,897,562 bp (18.65%) number of T's = 1,766,036,458 bp (30.33%) number of G's = 1,268,423,453 bp (21.78%) number of N's = 225,518 bp (0%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 66,548,460 number of insertions = 962,279 mapped reads with insertion percentage = 2.09% number of deletions = 2,038,707 mapped reads with deletion percentage = 4.49% homopolymer indels = 46.84% >>>>>>> Coverage mean coverageData = 1.8824X std coverageData = 25.1517X There is a 43.02% of reference with a coverageData >= 1X There is a 30.49% of reference with a coverageData >= 2X There is a 22.04% of reference with a coverageData >= 3X There is a 16.59% of reference with a coverageData >= 4X There is a 12.61% of reference with a coverageData >= 5X There is a 9.77% of reference with a coverageData >= 6X There is a 7.64% of reference with a coverageData >= 7X There is a 6.04% of reference with a coverageData >= 8X There is a 4.82% of reference with a coverageData >= 9X There is a 3.88% of reference with a coverageData >= 10X There is a 3.14% of reference with a coverageData >= 11X There is a 2.56% of reference with a coverageData >= 12X There is a 2.1% of reference with a coverageData >= 13X There is a 1.73% of reference with a coverageData >= 14X There is a 1.44% of reference with a coverageData >= 15X There is a 1.2% of reference with a coverageData >= 16X There is a 1.01% of reference with a coverageData >= 17X There is a 0.85% of reference with a coverageData >= 18X There is a 0.72% of reference with a coverageData >= 19X There is a 0.61% of reference with a coverageData >= 20X There is a 0.52% of reference with a coverageData >= 21X There is a 0.45% of reference with a coverageData >= 22X There is a 0.38% of reference with a coverageData >= 23X There is a 0.33% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.15% of reference with a coverageData >= 30X There is a 0.14% of reference with a coverageData >= 31X There is a 0.12% of reference with a coverageData >= 32X There is a 0.11% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.08% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 501540530 2.0121937028193 22.07956753873338 chr2 243199373 535604328 2.2023261055035697 25.90568452293102 chr3 198022430 404726363 2.0438410083140583 4.097156472309409 chr4 191154276 412516993 2.158031730349574 19.87252488033933 chr5 180915260 286533620 1.5838001725227602 3.776442503291432 chr6 171115067 337604711 1.972968932069553 13.253727662457052 chr7 159138663 320126478 2.011619753271397 28.557527364280293 chr8 146364022 306798223 2.0961314044786223 7.301734996234449 chr9 141213431 253035802 1.7918678146131866 50.50034067881908 chr10 135534747 325180311 2.399239443742054 68.51804230162924 chr11 135006516 273920138 2.028940129082362 13.728807364588542 chr12 133851895 255494605 1.9087858636592332 8.264995812605783 chr13 115169878 143721369 1.2479076256380162 2.8375960854902975 chr14 107349540 172785297 1.6095578704855187 3.9187454853924346 chr15 102531392 155410843 1.5157391308995396 4.651553427143086 chr16 90354753 202561359 2.2418450858916077 37.026416072835616 chr17 81195210 95726344 1.178965409412698 16.659876069558116 chr18 78077248 268007756 3.432597368185928 42.61978813208573 chr19 59128983 70678288 1.195323924309674 12.141007680710976 chr20 63025520 112413656 1.7836212378731664 6.797057586752174 chr21 48129895 74601577 1.5500049813115113 10.29230839423181 chr22 51304566 44555510 0.8684511628068348 2.6677656563267487 chrMT 16571 881982 53.22442821797115 28.598780190663252 chrX 155270560 189611185 1.2211663627670306 5.369363237086219 chrY 59373566 83145358 1.4003766928872017 36.32379500331283