BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779310.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 = 18,574,426 number of mapped reads = 17,657,864 (95.07%) number of supplementary alignments = 43,035 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,912,148 number of mapped paired reads (second in pair) = 8,745,716 number of mapped paired reads (both in pair) = 17,462,926 number of mapped paired reads (singletons) = 194,938 number of mapped bases = 1,405,807,344 bp number of sequenced bases = 1,405,530,995 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 559,810 duplication rate = 3.01% >>>>>>> Insert size mean insert size = 30,266.3813 std insert size = 1,614,014.2781 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 53.4763 >>>>>>> ACTG content number of A's = 434,154,239 bp (30.89%) number of C's = 266,509,167 bp (18.96%) number of T's = 433,742,148 bp (30.86%) number of G's = 270,757,293 bp (19.26%) number of N's = 368,148 bp (0.03%) GC percentage = 38.23% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 4,924,663 number of insertions = 102,647 mapped reads with insertion percentage = 0.58% number of deletions = 131,153 mapped reads with deletion percentage = 0.73% homopolymer indels = 47.06% >>>>>>> Coverage mean coverageData = 0.4541X std coverageData = 1.5438X There is a 19.84% of reference with a coverageData >= 1X There is a 8.89% of reference with a coverageData >= 2X There is a 4.88% of reference with a coverageData >= 3X There is a 3.02% of reference with a coverageData >= 4X There is a 2.01% of reference with a coverageData >= 5X There is a 1.41% of reference with a coverageData >= 6X There is a 1.03% of reference with a coverageData >= 7X There is a 0.77% of reference with a coverageData >= 8X There is a 0.59% of reference with a coverageData >= 9X There is a 0.47% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 83355271 0.3344235238635574 1.2200250712599092 chr2 243199373 93041615 0.3825734164207734 1.3361781486293056 chr3 198022430 97787504 0.49382034146333825 1.457556811116811 chr4 191154276 123488067 0.6460125799121543 1.8079612987572857 chr5 180915260 99632976 0.5507162635147527 1.7933230333879142 chr6 171115067 73608722 0.43017089780878265 1.4225800013668166 chr7 159138663 127134270 0.798889896416938 2.4871447856821343 chr8 146364022 119045846 0.8133545687887697 2.122185288564323 chr9 141213431 59355650 0.4203258116432282 1.3662676300423775 chr10 135534747 27581867 0.20350402838026474 0.9554442383900078 chr11 135006516 49857341 0.3692958123591605 1.2174362949490751 chr12 133851895 70998058 0.5304225091471436 1.4961454877038836 chr13 115169878 58653886 0.5092814807010563 1.5004958351696467 chr14 107349540 41308941 0.38480780634924006 1.2294324072234961 chr15 102531392 36655385 0.3575040217926623 1.4585861741661459 chr16 90354753 28290938 0.313109571557348 1.088097765942377 chr17 81195210 21877986 0.26944921997245896 1.4163649006198566 chr18 78077248 42248726 0.5411144357956879 1.6435435581146545 chr19 59128983 14961225 0.2530269292810262 0.9564949600094034 chr20 63025520 31158504 0.49437916577284885 1.6905963040316356 chr21 48129895 19535826 0.40589795593778044 1.4417416670857663 chr22 51304566 6122195 0.11933041203389187 0.6623180725856269 chrMT 16571 4063 0.2451873755355742 0.6436350744466387 chrX 155270560 79428276 0.5115475593055117 1.7950051451152065 chrY 59373566 674206 0.01135532267002457 0.16049173869649708