BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779295.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 = 21,468,708 number of mapped reads = 20,939,664 (97.54%) number of supplementary alignments = 54,895 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,536,235 number of mapped paired reads (second in pair) = 10,403,429 number of mapped paired reads (both in pair) = 20,774,348 number of mapped paired reads (singletons) = 165,316 number of mapped bases = 1,667,303,113 bp number of sequenced bases = 1,666,982,557 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 918,307 duplication rate = 3.84% >>>>>>> Insert size mean insert size = 45,817.9797 std insert size = 2,006,293.362 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.9895 >>>>>>> ACTG content number of A's = 513,365,495 bp (30.8%) number of C's = 318,845,741 bp (19.13%) number of T's = 509,169,146 bp (30.54%) number of G's = 325,159,846 bp (19.51%) number of N's = 442,329 bp (0.03%) GC percentage = 38.63% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 5,597,924 number of insertions = 118,530 mapped reads with insertion percentage = 0.56% number of deletions = 153,208 mapped reads with deletion percentage = 0.72% homopolymer indels = 46.68% >>>>>>> Coverage mean coverageData = 0.5386X std coverageData = 2.1868X There is a 19.99% of reference with a coverageData >= 1X There is a 10.35% of reference with a coverageData >= 2X There is a 6.21% of reference with a coverageData >= 3X There is a 4.07% of reference with a coverageData >= 4X There is a 2.82% of reference with a coverageData >= 5X There is a 2.03% of reference with a coverageData >= 6X There is a 1.5% of reference with a coverageData >= 7X There is a 1.14% of reference with a coverageData >= 8X There is a 0.88% of reference with a coverageData >= 9X There is a 0.69% of reference with a coverageData >= 10X There is a 0.55% of reference with a coverageData >= 11X There is a 0.44% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 123208209 0.49431455177798733 2.4949589863440274 chr2 243199373 145103995 0.5966462545115196 1.8603487009638464 chr3 198022430 133775946 0.6755595616112781 1.913626320052173 chr4 191154276 127020276 0.6644908953017614 1.9117238687046798 chr5 180915260 116941899 0.646390464795507 1.8005616481524238 chr6 171115067 101702894 0.5943538215720069 1.8653794584496075 chr7 159138663 135617704 0.8521983372450478 5.477575171657264 chr8 146364022 115566040 0.7895795593810615 2.1223819918622544 chr9 141213431 59717118 0.42288553983225574 1.5988355591495627 chr10 135534747 28606597 0.2110646725890889 2.215214372360359 chr11 135006516 63298357 0.4688540884945139 1.542882140505808 chr12 133851895 78179877 0.5840774760790648 1.83467396297534 chr13 115169878 53931406 0.4682770090283503 1.4813744671815723 chr14 107349540 45588358 0.42467213180419777 1.413146005050259 chr15 102531392 38656471 0.3770208347507854 1.2795286304515832 chr16 90354753 25284898 0.27984026473958706 1.0488296430698816 chr17 81195210 27632239 0.34031858529585673 1.3611731015222008 chr18 78077248 28467431 0.3646059733047968 1.1986650927049163 chr19 59128983 15413398 0.2606741604197725 1.38118460655807 chr20 63025520 33333583 0.5288902495370129 1.7579711105156806 chr21 48129895 15260583 0.3170707727494523 1.3474217070703007 chr22 51304566 7700148 0.1500869922571804 0.7290132337447768 chrMT 16571 2055 0.12401182789210066 0.3694765565162187 chrX 155270560 145789580 0.9389389720755821 2.5671186970590405 chrY 59373566 1504051 0.025331997070885046 0.3333958389864506