BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525187.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 = 1,452,653 number of mapped reads = 1,351,689 (93.05%) number of supplementary alignments = 4,299 (0.3%) number of secondary alignments = 0 number of mapped bases = 81,014,074 bp number of sequenced bases = 80,986,018 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,573 duplication rate = 1.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.523 >>>>>>> ACTG content number of A's = 21,342,258 bp (26.35%) number of C's = 16,220,780 bp (20.03%) number of T's = 24,781,743 bp (30.6%) number of G's = 18,639,320 bp (23.02%) number of N's = 1,917 bp (0%) GC percentage = 43.04% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 405,939 number of insertions = 5,271 mapped reads with insertion percentage = 0.39% number of deletions = 17,501 mapped reads with deletion percentage = 1.29% homopolymer indels = 43.65% >>>>>>> Coverage mean coverageData = 0.0262X std coverageData = 0.2642X There is a 2.41% 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 8904258 0.03572411560812119 0.5303636809029207 chr2 243199373 6895358 0.0283526964520587 0.30455430782601417 chr3 198022430 6592333 0.03329083983061919 0.19581804299647376 chr4 191154276 4550861 0.023807267591544747 0.1704531014880015 chr5 180915260 3741653 0.02068179876036991 0.15293370447287205 chr6 171115067 4175290 0.024400481343936825 0.19168962023152702 chr7 159138663 4845499 0.030448282702990912 0.38807687194132295 chr8 146364022 3823355 0.026122232415832357 0.21011348232933202 chr9 141213431 2723825 0.019288710575979136 0.1923070486582252 chr10 135534747 4568431 0.033706714337984486 0.3038106398637043 chr11 135006516 3804290 0.028178565840481357 0.21883320411403787 chr12 133851895 3788189 0.02830134754535974 0.18143317306503332 chr13 115169878 2550291 0.02214373275623336 0.15951079671171733 chr14 107349540 3140218 0.029252272529532962 0.18633638349257542 chr15 102531392 2282384 0.022260343446814806 0.1585430893149812 chr16 90354753 2255694 0.02496486266749022 0.18504265948000057 chr17 81195210 1697689 0.020908733409273773 0.15968465128443832 chr18 78077248 1783137 0.02283811283922302 0.3338735445958151 chr19 59128983 1500235 0.02537224426809438 0.3593841208928349 chr20 63025520 1541088 0.024451809362302762 0.1676692358240956 chr21 48129895 781560 0.016238556099073143 0.14608530606037323 chr22 51304566 679480 0.013244045374051112 0.12131757268238783 chrMT 16571 11634 0.7020698811176151 1.0002873023663523 chrX 155270560 4144258 0.026690558725363005 0.18700466145431346 chrY 59373566 233064 0.003925383225255495 0.12390416869248318