BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960894.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 = 225,779,896 number of mapped reads = 221,957,500 (98.31%) number of supplementary alignments = 386,955 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 111,249,241 number of mapped paired reads (second in pair) = 110,708,259 number of mapped paired reads (both in pair) = 220,654,844 number of mapped paired reads (singletons) = 1,302,656 number of mapped bases = 21,771,841,763 bp number of sequenced bases = 21,765,489,975 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,812,806 duplication rate = 9.69% >>>>>>> Insert size mean insert size = 15,558.6969 std insert size = 1,168,827.2418 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 53.6281 >>>>>>> ACTG content number of A's = 6,637,539,993 bp (30.5%) number of C's = 4,251,674,028 bp (19.53%) number of T's = 6,626,426,066 bp (30.44%) number of G's = 4,248,612,887 bp (19.52%) number of N's = 1,237,001 bp (0.01%) GC percentage = 39.05% >>>>>>> Mismatches and indels general error rate = 0.0126 number of mismatches = 267,965,045 number of insertions = 2,605,884 mapped reads with insertion percentage = 1.14% number of deletions = 2,761,078 mapped reads with deletion percentage = 1.21% homopolymer indels = 40.66% >>>>>>> Coverage mean coverageData = 7.0329X std coverageData = 94.3266X There is a 89.52% of reference with a coverageData >= 1X There is a 85.48% of reference with a coverageData >= 2X There is a 79.43% of reference with a coverageData >= 3X There is a 71.88% of reference with a coverageData >= 4X There is a 63.41% of reference with a coverageData >= 5X There is a 54.66% of reference with a coverageData >= 6X There is a 46.14% of reference with a coverageData >= 7X There is a 38.21% of reference with a coverageData >= 8X There is a 31.1% of reference with a coverageData >= 9X There is a 24.91% of reference with a coverageData >= 10X There is a 19.66% of reference with a coverageData >= 11X There is a 15.3% of reference with a coverageData >= 12X There is a 11.76% of reference with a coverageData >= 13X There is a 8.94% of reference with a coverageData >= 14X There is a 6.73% of reference with a coverageData >= 15X There is a 5.03% of reference with a coverageData >= 16X There is a 3.73% of reference with a coverageData >= 17X There is a 2.76% of reference with a coverageData >= 18X There is a 2.04% of reference with a coverageData >= 19X There is a 1.51% of reference with a coverageData >= 20X There is a 1.13% of reference with a coverageData >= 21X There is a 0.85% of reference with a coverageData >= 22X There is a 0.65% of reference with a coverageData >= 23X There is a 0.5% of reference with a coverageData >= 24X There is a 0.4% of reference with a coverageData >= 25X There is a 0.32% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1847093395 7.4105869329007605 235.56811839620252 chr2 243199373 2285406747 9.397255917267517 50.45044035267184 chr3 198022430 1428790115 7.215294322971393 13.824459153310872 chr4 191154276 1210096679 6.330471409386625 76.17538474168458 chr5 180915260 1174553294 6.492284255070579 8.286131600950894 chr6 171115067 1332644297 7.788000907015395 27.66563826959145 chr7 159138663 1129011851 7.094516377833337 59.89742080113795 chr8 146364022 1242492211 8.489054851198336 93.55690354158773 chr9 141213431 1102964245 7.810618559363522 76.80981959331196 chr10 135534747 965494428 7.123593391147143 220.98274490085058 chr11 135006516 966130887 7.156179683949477 36.97121125611301 chr12 133851895 1100588789 8.22243711230237 7.8834554059688 chr13 115169878 611239423 5.30728549525771 4.71922446981269 chr14 107349540 432665262 4.030434243127637 6.854601120802679 chr15 102531392 533519651 5.203476131485663 4.630954147906406 chr16 90354753 591795153 6.5496848073946925 85.52401660312819 chr17 81195210 467284186 5.75507084715958 24.474094869359536 chr18 78077248 686345676 8.79059769114813 80.78438002444153 chr19 59128983 382315277 6.465784757366789 103.15576841780164 chr20 63025520 423709446 6.722823484835984 22.269461876044208 chr21 48129895 271901296 5.649322442943206 30.77750052697528 chr22 51304566 253056884 4.932443712709703 6.224112646233566 chrMT 16571 8717123 526.0468891436848 109.31899979523682 chrX 155270560 1263686446 8.138609444056877 26.069271245432414 chrY 59373566 60339002 1.0162603674503903 65.18944966604307