BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004105.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 = 2,986,981 number of mapped reads = 2,176,553 (72.87%) number of supplementary alignments = 18,355 (0.61%) number of secondary alignments = 0 number of mapped bases = 141,433,773 bp number of sequenced bases = 141,365,999 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 297,374 duplication rate = 10.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1609 >>>>>>> ACTG content number of A's = 38,150,651 bp (26.99%) number of C's = 25,380,747 bp (17.95%) number of T's = 46,659,866 bp (33.01%) number of G's = 31,156,207 bp (22.04%) number of N's = 18,528 bp (0.01%) GC percentage = 39.99% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,462,788 number of insertions = 11,810 mapped reads with insertion percentage = 0.54% number of deletions = 41,599 mapped reads with deletion percentage = 1.89% homopolymer indels = 47.51% >>>>>>> Coverage mean coverageData = 0.0457X std coverageData = 0.4776X There is a 2.46% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% 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% 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 11241730 0.04510211430927588 0.6735231875909553 chr2 243199373 12050082 0.04954816228082957 0.5183490509194041 chr3 198022430 8852429 0.044704173158565924 0.3519689831863435 chr4 191154276 10519011 0.055028907645257176 0.40722112994532195 chr5 180915260 8931064 0.04936600704661398 0.3745267719791999 chr6 171115067 9624463 0.05624556135667469 0.42171131297823994 chr7 159138663 8088913 0.05082933868811 0.5295739112098725 chr8 146364022 9075757 0.062008114261850496 0.9479150361152987 chr9 141213431 5480303 0.03880865269819837 0.4090801484712944 chr10 135534747 6444398 0.047547939865191916 0.42798663084899163 chr11 135006516 6402680 0.04742497021403026 0.42446273076571006 chr12 133851895 5416203 0.040464148826581794 0.3411514034780163 chr13 115169878 4666104 0.040514968679570884 0.34107063324870984 chr14 107349540 4361326 0.04062733757405947 0.35068289129616814 chr15 102531392 3716564 0.03624805952112695 0.32059789119362175 chr16 90354753 3522288 0.03898287453677174 0.34187155237629363 chr17 81195210 2991461 0.03684282607311441 0.33354155635927074 chr18 78077248 4385853 0.05617325293022623 0.7158748222712543 chr19 59128983 2172124 0.03673535193392384 0.47155797320423426 chr20 63025520 3142120 0.04985472551436307 0.3831204227783175 chr21 48129895 2130652 0.044268785543787284 0.36488268117632716 chr22 51304566 1360093 0.026510174552494995 0.27317872805047955 chrMT 16571 88538 5.342948524530807 5.028843062568534 chrX 155270560 5587868 0.03598794259517065 0.3224571251539083 chrY 59373566 1181749 0.01990362175652377 0.2760259736505408