BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504596.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 364,671,172 number of mapped reads = 348,913,207 (95.68%) number of supplementary alignments = 1,018,060 (0.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 174,584,715 number of mapped paired reads (second in pair) = 174,328,492 number of mapped paired reads (both in pair) = 345,965,020 number of mapped paired reads (singletons) = 2,948,187 number of mapped bases = 33,519,765,941 bp number of sequenced bases = 33,509,022,153 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,794,945 duplication rate = 18.03% >>>>>>> Insert size mean insert size = 34,124.921 std insert size = 1,752,241.8094 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 53.3716 >>>>>>> ACTG content number of A's = 9,521,361,583 bp (28.41%) number of C's = 7,187,358,030 bp (21.45%) number of T's = 9,426,271,120 bp (28.13%) number of G's = 7,364,645,828 bp (21.98%) number of N's = 9,385,592 bp (0.03%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 186,301,201 number of insertions = 3,387,822 mapped reads with insertion percentage = 0.93% number of deletions = 4,157,302 mapped reads with deletion percentage = 1.15% homopolymer indels = 40.41% >>>>>>> Coverage mean coverageData = 10.8279X std coverageData = 95.3997X There is a 90.88% of reference with a coverageData >= 1X There is a 89.12% of reference with a coverageData >= 2X There is a 86.15% of reference with a coverageData >= 3X There is a 81.99% of reference with a coverageData >= 4X There is a 76.79% of reference with a coverageData >= 5X There is a 70.85% of reference with a coverageData >= 6X There is a 64.45% of reference with a coverageData >= 7X There is a 57.89% of reference with a coverageData >= 8X There is a 51.43% of reference with a coverageData >= 9X There is a 45.24% of reference with a coverageData >= 10X There is a 39.47% of reference with a coverageData >= 11X There is a 34.19% of reference with a coverageData >= 12X There is a 29.46% of reference with a coverageData >= 13X There is a 25.27% of reference with a coverageData >= 14X There is a 21.61% of reference with a coverageData >= 15X There is a 18.44% of reference with a coverageData >= 16X There is a 15.73% of reference with a coverageData >= 17X There is a 13.42% of reference with a coverageData >= 18X There is a 11.47% of reference with a coverageData >= 19X There is a 9.83% of reference with a coverageData >= 20X There is a 8.45% of reference with a coverageData >= 21X There is a 7.3% of reference with a coverageData >= 22X There is a 6.33% of reference with a coverageData >= 23X There is a 5.52% of reference with a coverageData >= 24X There is a 4.84% of reference with a coverageData >= 25X There is a 4.27% of reference with a coverageData >= 26X There is a 3.8% of reference with a coverageData >= 27X There is a 3.39% of reference with a coverageData >= 28X There is a 3.05% of reference with a coverageData >= 29X There is a 2.76% of reference with a coverageData >= 30X There is a 2.51% of reference with a coverageData >= 31X There is a 2.3% of reference with a coverageData >= 32X There is a 2.12% of reference with a coverageData >= 33X There is a 1.96% of reference with a coverageData >= 34X There is a 1.82% of reference with a coverageData >= 35X There is a 1.69% of reference with a coverageData >= 36X There is a 1.59% of reference with a coverageData >= 37X There is a 1.49% of reference with a coverageData >= 38X There is a 1.4% of reference with a coverageData >= 39X There is a 1.32% of reference with a coverageData >= 40X There is a 1.25% of reference with a coverageData >= 41X There is a 1.19% of reference with a coverageData >= 42X There is a 1.13% of reference with a coverageData >= 43X There is a 1.08% of reference with a coverageData >= 44X There is a 1.03% of reference with a coverageData >= 45X There is a 0.98% of reference with a coverageData >= 46X There is a 0.94% of reference with a coverageData >= 47X There is a 0.9% of reference with a coverageData >= 48X There is a 0.87% of reference with a coverageData >= 49X There is a 0.83% of reference with a coverageData >= 50X There is a 0.8% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3118128053 12.510011170644185 173.06090616569793 chr2 243199373 2366526861 9.730809877540269 57.65033344895087 chr3 198022430 1981862752 10.008274072790643 16.571626223374572 chr4 191154276 1899223195 9.93555171635292 114.40013548046335 chr5 180915260 1583088398 8.75044149399006 10.272002073929789 chr6 171115067 1570781895 9.179681968040839 22.611532179521074 chr7 159138663 2827866375 17.769826148407443 137.38307226684344 chr8 146364022 2947042490 20.135019861643322 67.15816063346142 chr9 141213431 1208431198 8.557480612449675 60.90376368056249 chr10 135534747 1631621129 12.03839727534962 258.4859110444758 chr11 135006516 1439079073 10.659330494833302 38.84771791209031 chr12 133851895 1252583884 9.357983941878446 9.045160281646124 chr13 115169878 813961785 7.067488471247664 6.514789574331795 chr14 107349540 1087549980 10.13092352328664 9.532898640229426 chr15 102531392 875590320 8.53972917874752 7.3241445249330654 chr16 90354753 931473592 10.309071311389673 73.52380488674287 chr17 81195210 1039979014 12.808378893286932 45.15194763330685 chr18 78077248 571818967 7.3237592467398445 94.41469958348164 chr19 59128983 670431237 11.338453715667661 89.32066166609303 chr20 63025520 1409029956 22.356498700843723 29.258718673470526 chr21 48129895 402260656 8.357812872851685 40.265485687186384 chr22 51304566 452229333 8.814602057056677 9.465030975942792 chrMT 16571 119926369 7237.123227324844 1547.8824157821607 chrX 155270560 1190582369 7.667792072109484 18.739674971070563 chrY 59373566 128697060 2.167581782101483 116.07258484281974