BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779394.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 15,039,106 number of mapped reads = 14,336,535 (95.33%) number of supplementary alignments = 54,813 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,208,626 number of mapped paired reads (second in pair) = 7,127,909 number of mapped paired reads (both in pair) = 14,215,646 number of mapped paired reads (singletons) = 120,889 number of mapped bases = 1,138,098,966 bp number of sequenced bases = 1,137,826,021 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 530,297 duplication rate = 3.41% >>>>>>> Insert size mean insert size = 149,206.41 std insert size = 3,743,204.8317 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 53.1423 >>>>>>> ACTG content number of A's = 342,962,969 bp (30.14%) number of C's = 225,688,154 bp (19.84%) number of T's = 338,872,313 bp (29.78%) number of G's = 230,051,674 bp (20.22%) number of N's = 250,911 bp (0.02%) GC percentage = 40.05% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 3,803,939 number of insertions = 109,105 mapped reads with insertion percentage = 0.75% number of deletions = 128,876 mapped reads with deletion percentage = 0.89% homopolymer indels = 46.99% >>>>>>> Coverage mean coverageData = 0.3676X std coverageData = 1.3363X There is a 17.4% of reference with a coverageData >= 1X There is a 8.37% of reference with a coverageData >= 2X There is a 4.34% of reference with a coverageData >= 3X There is a 2.44% of reference with a coverageData >= 4X There is a 1.43% of reference with a coverageData >= 5X There is a 0.87% of reference with a coverageData >= 6X There is a 0.55% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 85806308 0.3442571483101741 2.215272567629451 chr2 243199373 103376170 0.42506758436420805 1.2390983340843134 chr3 198022430 90964586 0.4593650628365686 1.2166809114037551 chr4 191154276 83921147 0.43902312182647696 1.139194525584868 chr5 180915260 104741216 0.5789518031812242 1.3446336678396167 chr6 171115067 46748577 0.2731996534238566 1.1153124627170166 chr7 159138663 150560359 0.9460954124014477 2.220806439074716 chr8 146364022 53882025 0.36813708904501136 1.0498777634981051 chr9 141213431 55883939 0.39574096177862855 1.4451046044444114 chr10 135534747 22059050 0.16275568065213564 1.4422022764891091 chr11 135006516 54645364 0.4047609376128186 1.2101340589692413 chr12 133851895 49107297 0.366877861534945 1.0308222003110101 chr13 115169878 32680337 0.28375767663833074 0.9080428768443972 chr14 107349540 34384145 0.3203008135852282 1.0027306686527142 chr15 102531392 21911941 0.21370958271979765 0.7922081096661928 chr16 90354753 18645645 0.20636042245613798 0.8225984378276765 chr17 81195210 20672930 0.25460775333914404 1.0587771993270885 chr18 78077248 33075949 0.42363108136188404 1.456644368010237 chr19 59128983 11028513 0.18651619629581656 1.3555107700788918 chr20 63025520 19647000 0.3117308671154161 1.0073300919630466 chr21 48129895 11897343 0.24719237388737292 0.8886120722608662 chr22 51304566 5741808 0.11191612068212409 0.5734543748011554 chrMT 16571 1493 0.09009715768511255 0.34395956971701064 chrX 155270560 22349719 0.14394048041045257 0.6476387875092163 chrY 59373566 4366105 0.07353617601476051 0.43727462537010764