BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779409.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 = 14,913,022 number of mapped reads = 14,567,888 (97.69%) number of supplementary alignments = 52,064 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,340,855 number of mapped paired reads (second in pair) = 7,227,033 number of mapped paired reads (both in pair) = 14,428,550 number of mapped paired reads (singletons) = 139,338 number of mapped bases = 1,158,574,466 bp number of sequenced bases = 1,158,331,408 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 483,066 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 176,707.7835 std insert size = 4,022,838.1003 median insert size = 181 >>>>>>> Mapping quality mean mapping quality = 53.4353 >>>>>>> ACTG content number of A's = 354,069,150 bp (30.57%) number of C's = 225,786,484 bp (19.49%) number of T's = 346,313,516 bp (29.9%) number of G's = 231,906,106 bp (20.02%) number of N's = 256,152 bp (0.02%) GC percentage = 39.51% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 3,768,936 number of insertions = 100,347 mapped reads with insertion percentage = 0.68% number of deletions = 117,134 mapped reads with deletion percentage = 0.79% homopolymer indels = 47.28% >>>>>>> Coverage mean coverageData = 0.3743X std coverageData = 1.4577X There is a 20.9% of reference with a coverageData >= 1X There is a 8.51% of reference with a coverageData >= 2X There is a 3.65% of reference with a coverageData >= 3X There is a 1.7% of reference with a coverageData >= 4X There is a 0.85% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% 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 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 92614660 0.37157243431702425 3.348269095603584 chr2 243199373 97047375 0.3990445115168944 0.9578867402619893 chr3 198022430 84022510 0.4243080442957901 0.9419682164782701 chr4 191154276 69338154 0.3627339939808618 0.8549939580339715 chr5 180915260 104697547 0.5787104249801813 1.0944686079964512 chr6 171115067 50650830 0.29600450087776314 1.1481012131145112 chr7 159138663 136074219 0.8550669990233611 2.2312461575940596 chr8 146364022 64434848 0.4402369319968537 0.9670542155883274 chr9 141213431 68125419 0.48242874999616714 1.7742245475246896 chr10 135534747 35994479 0.26557380890673005 1.6071793334652673 chr11 135006516 51616333 0.38232475386595416 0.9441395303163288 chr12 133851895 53666540 0.40093971026708286 0.9277670304904183 chr13 115169878 40807855 0.35432750045979905 0.8528653301507633 chr14 107349540 30919839 0.28802954348942716 0.7919771531935152 chr15 102531392 21965883 0.2142356850085484 0.6880352803374101 chr16 90354753 11737087 0.12990005074774538 0.5451431406620151 chr17 81195210 20387772 0.2510957481358814 0.778021748948076 chr18 78077248 30653396 0.3926034380719976 1.0289808935189126 chr19 59128983 10368320 0.17535089348653266 1.9564210019796793 chr20 63025520 19869168 0.31525591538157877 0.8229854088625668 chr21 48129895 15287791 0.3176360762889676 0.8876664826575417 chr22 51304566 8407154 0.16386755907846487 0.61454695472767 chrMT 16571 1390 0.08388147969344034 0.43066097564264066 chrX 155270560 35304065 0.2273712737301907 0.6965588006135043 chrY 59373566 4581832 0.07716956060884064 0.4039783317431718