BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234028.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,133,983 number of mapped reads = 191,955 (16.93%) number of supplementary alignments = 2,049 (0.18%) number of secondary alignments = 0 number of mapped bases = 11,455,801 bp number of sequenced bases = 11,449,579 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,719 duplication rate = 5.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.1739 >>>>>>> ACTG content number of A's = 3,056,589 bp (26.7%) number of C's = 1,944,748 bp (16.99%) number of T's = 3,820,449 bp (33.37%) number of G's = 2,626,799 bp (22.94%) number of N's = 994 bp (0.01%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 111,422 number of insertions = 1,781 mapped reads with insertion percentage = 0.91% number of deletions = 3,498 mapped reads with deletion percentage = 1.79% homopolymer indels = 37.3% >>>>>>> Coverage mean coverageData = 0.0037X std coverageData = 0.1831X There is a 0.3% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 866272 0.0034755058844968736 0.0852798701816864 chr2 243199373 905176 0.003721950385127021 0.14078329756301672 chr3 198022430 836351 0.004223516497600802 0.10201835840144988 chr4 191154276 659250 0.0034487850012834657 0.08647680293578135 chr5 180915260 648656 0.0035854134139928274 0.08345515115288761 chr6 171115067 890505 0.005204129686604395 0.10950462335967223 chr7 159138663 769268 0.004833947863442839 0.1520840567440942 chr8 146364022 699689 0.0047804712554291515 0.10537413926529231 chr9 141213431 484564 0.003431429974957552 0.07839241935960078 chr10 135534747 466451 0.0034415602664606736 0.08005872849026861 chr11 135006516 482529 0.003574116378205034 0.0783063304840637 chr12 133851895 464395 0.003469468997805373 0.12019779493925685 chr13 115169878 410042 0.003560323299118195 0.09943796924094364 chr14 107349540 398231 0.0037096665714636506 0.08393092101103401 chr15 102531392 301095 0.002936612818052836 0.08547260818511052 chr16 90354753 293415 0.003247366522046715 0.0898960784810074 chr17 81195210 267942 0.0032999729910175735 0.07281685185442573 chr18 78077248 376898 0.004827244935682159 0.9763672943232177 chr19 59128983 177319 0.0029988508342854467 0.07640811607931607 chr20 63025520 217792 0.0034556160742505574 0.07846436823461633 chr21 48129895 160527 0.0033352867277188117 0.07220428790236515 chr22 51304566 130334 0.0025403976714275297 0.06317542087023001 chrMT 16571 4825 0.29117132339629476 0.6060270020095937 chrX 155270560 497306 0.003202835102803777 0.07877442844495111 chrY 59373566 46969 7.910759478384707E-4 0.05022115545520201