BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716261.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 = 1,587,456 number of mapped reads = 1,458,990 (91.91%) number of supplementary alignments = 10,151 (0.64%) number of secondary alignments = 0 number of mapped bases = 86,750,257 bp number of sequenced bases = 86,723,212 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,309 duplication rate = 3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2584 >>>>>>> ACTG content number of A's = 22,572,554 bp (26.03%) number of C's = 15,749,258 bp (18.16%) number of T's = 26,867,857 bp (30.98%) number of G's = 21,532,374 bp (24.83%) number of N's = 1,169 bp (0%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 429,947 number of insertions = 6,512 mapped reads with insertion percentage = 0.44% number of deletions = 16,763 mapped reads with deletion percentage = 1.14% homopolymer indels = 41.16% >>>>>>> Coverage mean coverageData = 0.028X std coverageData = 0.2631X There is a 2.47% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% 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 7311791 0.02933509642088314 0.35485666364182206 chr2 243199373 8596503 0.03534755412383403 0.3314548114637819 chr3 198022430 6363399 0.03213473847381834 0.20603139718117977 chr4 191154276 4888208 0.025572056782030866 0.2195116626240125 chr5 180915260 4406465 0.02435651365175055 0.1721522256887357 chr6 171115067 4809454 0.028106548910739694 0.1934926805740441 chr7 159138663 4284152 0.026920874658850187 0.43443366783648046 chr8 146364022 6251086 0.04270917070043347 0.34041801944943717 chr9 141213431 3710125 0.026273173689831245 0.2018609874826615 chr10 135534747 4273537 0.031530932802051125 0.39740274302055445 chr11 135006516 2605482 0.019298935171395727 0.17889601063253888 chr12 133851895 4092426 0.03057428510817871 0.21010658170636962 chr13 115169878 2252571 0.019558681828246792 0.15360015222509352 chr14 107349540 2844567 0.02649817595864873 0.18320591849898205 chr15 102531392 2115050 0.020628316447708035 0.16007255726608421 chr16 90354753 2738532 0.030308665665878143 0.1997668273039578 chr17 81195210 3797753 0.04677311629589972 0.2511647991251269 chr18 78077248 1951582 0.024995527506297355 0.2982585939399664 chr19 59128983 1828196 0.030918779712480426 0.3158179651082565 chr20 63025520 2055545 0.03261448695702947 0.2078933123983327 chr21 48129895 929555 0.019313464116221323 0.18052060778983262 chr22 51304566 1412905 0.02753955661568212 0.18402137266453672 chrMT 16571 10716 0.6466718966869833 0.9339043508158078 chrX 155270560 2985585 0.019228274825568995 0.16612332526105242 chrY 59373566 235072 0.003959202989424621 0.15295600381367114