BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124922.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,308,364 number of mapped reads = 4,234,455 (98.28%) number of supplementary alignments = 16,178 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,120,620 number of mapped paired reads (second in pair) = 2,113,835 number of mapped paired reads (both in pair) = 4,220,518 number of mapped paired reads (singletons) = 13,937 number of mapped bases = 367,410,201 bp number of sequenced bases = 367,217,352 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 303,409 duplication rate = 5.23% >>>>>>> Insert size mean insert size = 28,236.8847 std insert size = 1,543,744.4265 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 52.9058 >>>>>>> ACTG content number of A's = 103,660,479 bp (28.23%) number of C's = 67,884,929 bp (18.49%) number of T's = 109,254,638 bp (29.75%) number of G's = 86,412,527 bp (23.53%) number of N's = 4,779 bp (0%) GC percentage = 42.02% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 2,561,431 number of insertions = 48,733 mapped reads with insertion percentage = 1.12% number of deletions = 115,756 mapped reads with deletion percentage = 2.68% homopolymer indels = 47.92% >>>>>>> Coverage mean coverageData = 0.1187X std coverageData = 0.9794X There is a 8.49% of reference with a coverageData >= 1X There is a 2.12% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 24585066 0.0986359267686639 1.0787388990289808 chr2 243199373 31964557 0.13143355020080583 1.1321419397505348 chr3 198022430 24982673 0.1261608243066202 0.45164708546765153 chr4 191154276 18341743 0.09595256451391126 0.6416254039059889 chr5 180915260 21867881 0.12087361231993365 0.45047231459831527 chr6 171115067 20863262 0.12192533577420157 0.6441122645933223 chr7 159138663 22686902 0.14256059195369764 1.6777479415158387 chr8 146364022 17951709 0.12265110479131272 0.5151575031795965 chr9 141213431 15084088 0.10681765815887584 1.0299078028948143 chr10 135534747 17766637 0.13108547729092673 1.8388970274307312 chr11 135006516 21458107 0.15894126917548188 0.8938163123828695 chr12 133851895 21201591 0.158395897196674 0.514217799408669 chr13 115169878 7398311 0.06423824639286324 0.31192024094258175 chr14 107349540 11029611 0.1027448370994417 0.44178711278321287 chr15 102531392 10255540 0.10002341526778452 0.4041962556010154 chr16 90354753 12545162 0.13884340982039983 1.966577506182805 chr17 81195210 13269427 0.16342622920736333 1.7027234087946241 chr18 78077248 9890087 0.12667053787551527 1.2084576857055485 chr19 59128983 5050504 0.0854150324215791 0.6337286593691619 chr20 63025520 5741784 0.09110252481851797 0.4141822125635339 chr21 48129895 4597394 0.09552054913063908 0.48873749268583117 chr22 51304566 3852257 0.07508604594764529 0.3624807480684668 chrMT 16571 63385 3.8250558204091485 2.931726589611244 chrX 155270560 24147450 0.15551853487229003 0.644847383623048 chrY 59373566 815073 0.013727876813058525 0.7677655605306961