BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524956.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 = 3,164,118 number of mapped reads = 2,917,207 (92.2%) number of supplementary alignments = 13,660 (0.43%) number of secondary alignments = 0 number of mapped bases = 168,124,005 bp number of sequenced bases = 168,079,587 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,731 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1685 >>>>>>> ACTG content number of A's = 40,653,740 bp (24.19%) number of C's = 33,004,869 bp (19.64%) number of T's = 52,135,540 bp (31.02%) number of G's = 42,280,534 bp (25.16%) number of N's = 4,904 bp (0%) GC percentage = 44.79% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 790,838 number of insertions = 8,910 mapped reads with insertion percentage = 0.3% number of deletions = 26,005 mapped reads with deletion percentage = 0.89% homopolymer indels = 43.32% >>>>>>> Coverage mean coverageData = 0.0543X std coverageData = 0.4258X There is a 4.6% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 11985149 0.048084730749778155 0.7294325836585107 chr2 243199373 12959452 0.05328735777620611 0.4788043696133856 chr3 198022430 10408118 0.052560298346000504 0.25896432484495163 chr4 191154276 10251630 0.05363013694760352 0.3089314557342247 chr5 180915260 9048088 0.05001285132055748 0.25760540906268165 chr6 171115067 8726524 0.050997987219909745 0.2861510859568385 chr7 159138663 10883365 0.06838919464844316 0.5940297906585026 chr8 146364022 7497330 0.051223858825087495 0.404092269689606 chr9 141213431 7751775 0.05489403483157349 0.456411397534028 chr10 135534747 6429570 0.04743853618585351 0.4285302610201461 chr11 135006516 6435596 0.047668780668334555 0.35947018290716465 chr12 133851895 12677891 0.09471581257777487 0.4196648907576489 chr13 115169878 6237571 0.05415974305364811 0.2627006220824498 chr14 107349540 6027190 0.056145466482669604 0.30273485079432355 chr15 102531392 4453750 0.04343791606769564 0.23729891599195935 chr16 90354753 4771501 0.05280852242493541 0.2883219572765042 chr17 81195210 5073279 0.0624824912701131 0.2996784712806647 chr18 78077248 5284480 0.06768271340711189 0.7937845773205963 chr19 59128983 2870418 0.048545025710995234 0.5669843658028985 chr20 63025520 5299531 0.08408547839034093 0.3453984786151977 chr21 48129895 2017507 0.041917959721291725 0.2895604961201701 chr22 51304566 1707297 0.033277681366605846 0.2043176242311733 chrMT 16571 5983 0.3610524410114055 0.6660297543375604 chrX 155270560 8840017 0.056932988455763923 0.33096167072834787 chrY 59373566 480993 0.008101130391932328 0.18631236238610663