BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063532.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 = 4,581,855 number of mapped reads = 4,341,343 (94.75%) number of supplementary alignments = 42,665 (0.93%) number of secondary alignments = 0 number of mapped bases = 278,725,994 bp number of sequenced bases = 278,620,469 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 803,625 duplication rate = 14.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2186 >>>>>>> ACTG content number of A's = 72,628,752 bp (26.07%) number of C's = 50,587,324 bp (18.16%) number of T's = 90,078,844 bp (32.33%) number of G's = 65,293,881 bp (23.43%) number of N's = 31,668 bp (0.01%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,480,307 number of insertions = 17,972 mapped reads with insertion percentage = 0.41% number of deletions = 60,116 mapped reads with deletion percentage = 1.37% homopolymer indels = 44.12% >>>>>>> Coverage mean coverageData = 0.09X std coverageData = 0.8608X There is a 5.43% of reference with a coverageData >= 1X There is a 1.98% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.15% 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 0.01% 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% 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 29127128 0.11685879811709676 1.44169386416517 chr2 243199373 23756936 0.09768502158103837 1.6601394640345657 chr3 198022430 13877064 0.07007824315659594 0.4028654259005215 chr4 191154276 13997548 0.07322644459180186 0.5098554580790243 chr5 180915260 13831544 0.07645316376296836 0.42509931972370774 chr6 171115067 17728542 0.10360596708880113 0.6633394565091063 chr7 159138663 26199367 0.1646323181689669 1.1086135439906226 chr8 146364022 10569037 0.07221062154195243 0.8397273216636759 chr9 141213431 11670769 0.08264631003831356 0.6640278156217727 chr10 135534747 11189943 0.08256143348981941 0.6205935903923306 chr11 135006516 13823195 0.10238909505671563 0.6596595983911936 chr12 133851895 8653997 0.06465352619774266 0.41638501382346066 chr13 115169878 6689595 0.05808458874984655 0.4086675614719257 chr14 107349540 6252048 0.05824010051649965 0.39098166557831104 chr15 102531392 5330944 0.051993286114754005 0.3783155101234968 chr16 90354753 6823926 0.07552370819939046 0.4549522290697157 chr17 81195210 7770312 0.09569914284352488 0.5521998863767921 chr18 78077248 9445057 0.12097066997033502 1.227408697240218 chr19 59128983 3731014 0.06309958011623505 1.0465396315130382 chr20 63025520 4587063 0.07278104171135756 0.4455267392962292 chr21 48129895 4683119 0.09730166666683981 0.5204582871884362 chr22 51304566 2700171 0.05263022788264109 0.3401357544736974 chrMT 16571 456662 27.55790235954378 17.73503005694946 chrX 155270560 24872636 0.16018900170128839 0.6997216681763814 chrY 59373566 958377 0.01614147615792523 0.5205819998078063