BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779424.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 = 16,431,558 number of mapped reads = 3,508,021 (21.35%) number of supplementary alignments = 83,272 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,719,193 number of mapped paired reads (second in pair) = 1,788,828 number of mapped paired reads (both in pair) = 3,355,720 number of mapped paired reads (singletons) = 152,301 number of mapped bases = 272,966,281 bp number of sequenced bases = 272,932,327 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,368,962 duplication rate = 11.2% >>>>>>> Insert size mean insert size = 48,972.2589 std insert size = 2,049,027.9622 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 50.2219 >>>>>>> ACTG content number of A's = 81,821,783 bp (29.98%) number of C's = 53,996,477 bp (19.78%) number of T's = 80,209,694 bp (29.39%) number of G's = 56,847,686 bp (20.83%) number of N's = 56,687 bp (0.02%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 1,097,599 number of insertions = 30,778 mapped reads with insertion percentage = 0.87% number of deletions = 19,445 mapped reads with deletion percentage = 0.55% homopolymer indels = 36.4% >>>>>>> Coverage mean coverageData = 0.0882X std coverageData = 32.6791X There is a 2.16% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% 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 13326688 0.05346702024866771 9.540700493013738 chr2 243199373 25144667 0.1033911670487736 21.69282879068266 chr3 198022430 59310557 0.2995143378454653 101.5769858468217 chr4 191154276 13784590 0.07211238110101184 12.98054562857645 chr5 180915260 18790286 0.10386236075386897 17.363548096053265 chr6 171115067 11422605 0.06675394049315365 8.82708050103797 chr7 159138663 7664367 0.04816156460985223 3.6188223875470467 chr8 146364022 17604751 0.12028059054020802 27.631841940090585 chr9 141213431 37754605 0.267358456859532 76.2983458549863 chr10 135534747 5400561 0.03984632073722025 2.076460108013218 chr11 135006516 5379515 0.0398463360094412 2.6915519047221594 chr12 133851895 10392604 0.07764256157897503 9.414949517270705 chr13 115169878 9389088 0.08152381649653219 12.578626111841013 chr14 107349540 3381045 0.03149566360507926 1.8011327742182979 chr15 102531392 2947078 0.028743177504115033 1.381487986747623 chr16 90354753 4092419 0.0452927916254721 5.27766562549422 chr17 81195210 4028894 0.04961984826444811 3.576439937447153 chr18 78077248 3693395 0.04730436964171688 6.222044275847122 chr19 59128983 2705053 0.04574834307567915 6.2915448393858435 chr20 63025520 7303587 0.11588301056460938 26.253585637618016 chr21 48129895 1656139 0.03440977795609153 0.8444972107496216 chr22 51304566 1218334 0.02374708715009888 1.6260116043769213 chrMT 16571 730990 44.112606360509325 15.77446530320649 chrX 155270560 5091446 0.03279080078026382 5.614292493247908 chrY 59373566 753017 0.01268269788612663 0.38481924774652443