BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16362022.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 338,239,990 number of mapped reads = 326,323,285 (96.48%) number of supplementary alignments = 15,023,600 (4.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 164,444,821 number of mapped paired reads (second in pair) = 161,878,464 number of mapped paired reads (both in pair) = 322,987,202 number of mapped paired reads (singletons) = 3,336,083 number of mapped bases = 45,334,443,815 bp number of sequenced bases = 45,295,015,447 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,245,062 duplication rate = 31.76% >>>>>>> Insert size mean insert size = 167,807.3912 std insert size = 3,964,615.8473 median insert size = 257 >>>>>>> Mapping quality mean mapping quality = 53.7994 >>>>>>> ACTG content number of A's = 13,081,422,440 bp (28.88%) number of C's = 9,542,690,531 bp (21.07%) number of T's = 13,014,437,604 bp (28.73%) number of G's = 9,653,069,531 bp (21.31%) number of N's = 3,395,341 bp (0.01%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 419,308,724 number of insertions = 8,204,598 mapped reads with insertion percentage = 2.39% number of deletions = 21,280,698 mapped reads with deletion percentage = 6.25% homopolymer indels = 44.61% >>>>>>> Coverage mean coverageData = 14.6444X std coverageData = 153.035X There is a 92.1% of reference with a coverageData >= 1X There is a 91.77% of reference with a coverageData >= 2X There is a 91.17% of reference with a coverageData >= 3X There is a 90.22% of reference with a coverageData >= 4X There is a 88.79% of reference with a coverageData >= 5X There is a 86.81% of reference with a coverageData >= 6X There is a 84.2% of reference with a coverageData >= 7X There is a 80.93% of reference with a coverageData >= 8X There is a 77.02% of reference with a coverageData >= 9X There is a 72.51% of reference with a coverageData >= 10X There is a 67.51% of reference with a coverageData >= 11X There is a 62.13% of reference with a coverageData >= 12X There is a 56.52% of reference with a coverageData >= 13X There is a 50.82% of reference with a coverageData >= 14X There is a 45.18% of reference with a coverageData >= 15X There is a 39.73% of reference with a coverageData >= 16X There is a 34.56% of reference with a coverageData >= 17X There is a 29.76% of reference with a coverageData >= 18X There is a 25.37% of reference with a coverageData >= 19X There is a 21.44% of reference with a coverageData >= 20X There is a 17.96% of reference with a coverageData >= 21X There is a 14.93% of reference with a coverageData >= 22X There is a 12.32% of reference with a coverageData >= 23X There is a 10.1% of reference with a coverageData >= 24X There is a 8.23% of reference with a coverageData >= 25X There is a 6.67% of reference with a coverageData >= 26X There is a 5.39% of reference with a coverageData >= 27X There is a 4.35% of reference with a coverageData >= 28X There is a 3.5% of reference with a coverageData >= 29X There is a 2.81% of reference with a coverageData >= 30X There is a 2.27% of reference with a coverageData >= 31X There is a 1.83% of reference with a coverageData >= 32X There is a 1.49% of reference with a coverageData >= 33X There is a 1.22% of reference with a coverageData >= 34X There is a 1% of reference with a coverageData >= 35X There is a 0.84% of reference with a coverageData >= 36X There is a 0.71% of reference with a coverageData >= 37X There is a 0.6% of reference with a coverageData >= 38X There is a 0.52% of reference with a coverageData >= 39X There is a 0.46% of reference with a coverageData >= 40X There is a 0.41% of reference with a coverageData >= 41X There is a 0.37% of reference with a coverageData >= 42X There is a 0.34% of reference with a coverageData >= 43X There is a 0.31% of reference with a coverageData >= 44X There is a 0.29% of reference with a coverageData >= 45X There is a 0.27% of reference with a coverageData >= 46X There is a 0.25% of reference with a coverageData >= 47X There is a 0.24% of reference with a coverageData >= 48X There is a 0.23% of reference with a coverageData >= 49X There is a 0.22% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3742701241 15.015815110045402 338.03511718815315 chr2 243199373 3909559647 16.075533414306953 116.24921072304157 chr3 198022430 3033540934 15.319178408223756 18.24666247140191 chr4 191154276 3043119037 15.919701618393303 150.9453379481791 chr5 180915260 2757162035 15.240074469118857 11.117027612247 chr6 171115067 2622307965 15.324822126855725 56.940347876032575 chr7 159138663 2491205626 15.654307878657997 108.59399790313009 chr8 146364022 2275865775 15.549352524625212 153.52231450476322 chr9 141213431 1941651210 13.749763009440652 162.74426825469817 chr10 135534747 2403774043 17.735481831828704 344.94819629557617 chr11 135006516 2069098522 15.325915987640181 47.73765197464358 chr12 133851895 2038514066 15.22962424999661 9.824187422684249 chr13 115169878 1440335062 12.506178586036185 9.016820710216642 chr14 107349540 1372427803 12.784664033027063 12.03826385929937 chr15 102531392 1283918567 12.522199708358587 9.179845985735419 chr16 90354753 1440152313 15.938866138010471 99.9223492520664 chr17 81195210 1284492860 15.819810799183843 70.2650764883898 chr18 78077248 1242893248 15.918763530189999 158.52249378965163 chr19 59128983 944267269 15.969617962142186 196.39904489169803 chr20 63025520 951782687 15.101544374405796 42.16088107840993 chr21 48129895 632855431 13.148905290568367 76.70735014231835 chr22 51304566 564622257 11.005302276604386 43.57497468549076 chrMT 16571 173943186 10496.843039044114 1627.9714834025413 chrX 155270560 1231964329 7.934307244077693 21.85311414985856 chrY 59373566 442288702 7.449252787006258 192.27612801445756