BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525053.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,089,198 number of mapped reads = 942,632 (86.54%) number of supplementary alignments = 3,946 (0.36%) number of secondary alignments = 0 number of mapped bases = 57,335,037 bp number of sequenced bases = 57,315,946 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,443 duplication rate = 3.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8467 >>>>>>> ACTG content number of A's = 15,742,704 bp (27.47%) number of C's = 9,941,703 bp (17.35%) number of T's = 17,978,496 bp (31.37%) number of G's = 13,646,507 bp (23.81%) number of N's = 6,536 bp (0.01%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 272,305 number of insertions = 4,978 mapped reads with insertion percentage = 0.53% number of deletions = 11,873 mapped reads with deletion percentage = 1.25% homopolymer indels = 43.67% >>>>>>> Coverage mean coverageData = 0.0185X std coverageData = 0.202X There is a 1.65% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 4561092 0.01829922020535307 0.3375195352554468 chr2 243199373 5121613 0.021059318273818083 0.23556217987813882 chr3 198022430 3733808 0.018855480159495064 0.14932540619677218 chr4 191154276 3951123 0.02066981227247043 0.18944701128111757 chr5 180915260 3397584 0.018779974668803504 0.14985788131775107 chr6 171115067 3387674 0.01979763710696499 0.16233165737106048 chr7 159138663 3172605 0.019936104402234422 0.2071436686985387 chr8 146364022 3253581 0.022229376834151222 0.26241860763852953 chr9 141213431 2584158 0.018299661595220357 0.1779311457177417 chr10 135534747 2682003 0.01978830565124381 0.24219383308029432 chr11 135006516 2689925 0.019924408685577814 0.17650254998511056 chr12 133851895 2506853 0.018728558157506847 0.15252238001165122 chr13 115169878 1832435 0.015910714084458787 0.1371045614620822 chr14 107349540 1827862 0.017027199185017466 0.14526365328198926 chr15 102531392 1675328 0.016339659174821306 0.13835615530495735 chr16 90354753 1582074 0.017509582478743537 0.15038459988135175 chr17 81195210 1524662 0.01877773331702695 0.15801836769552877 chr18 78077248 2143045 0.027447752769154978 0.2804637697164402 chr19 59128983 1055932 0.017858111985453902 0.24094817072950084 chr20 63025520 1264396 0.020061651216840417 0.1600511215639688 chr21 48129895 731732 0.015203274389025781 0.16822008802929236 chr22 51304566 646441 0.01260006760411929 0.12197495701197829 chrMT 16571 59775 3.6072053587592783 2.6983271370876047 chrX 155270560 1761335 0.011343650721682204 0.1242094867889203 chrY 59373566 188001 0.003166409105358435 0.1543056469312816