BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618635.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 29,568,612 number of mapped reads = 23,920,811 (80.9%) number of supplementary alignments = 115,762 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,286,712 number of mapped paired reads (second in pair) = 11,634,099 number of mapped paired reads (both in pair) = 22,483,144 number of mapped paired reads (singletons) = 1,437,667 number of mapped bases = 2,205,479,351 bp number of sequenced bases = 2,203,975,526 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,915,952 duplication rate = 35.47% >>>>>>> Insert size mean insert size = 106,674.272 std insert size = 3,323,629.1846 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 52.16 >>>>>>> ACTG content number of A's = 595,636,659 bp (27.03%) number of C's = 483,147,356 bp (21.92%) number of T's = 606,632,419 bp (27.52%) number of G's = 517,059,041 bp (23.46%) number of N's = 1,500,051 bp (0.07%) GC percentage = 45.38% >>>>>>> Mismatches and indels general error rate = 0.0141 number of mismatches = 30,512,677 number of insertions = 417,091 mapped reads with insertion percentage = 1.71% number of deletions = 1,061,118 mapped reads with deletion percentage = 4.33% homopolymer indels = 51.64% >>>>>>> Coverage mean coverageData = 0.7124X std coverageData = 5.0901X There is a 14.79% of reference with a coverageData >= 1X There is a 9.68% of reference with a coverageData >= 2X There is a 7.05% of reference with a coverageData >= 3X There is a 5.49% of reference with a coverageData >= 4X There is a 4.37% of reference with a coverageData >= 5X There is a 3.59% of reference with a coverageData >= 6X There is a 2.97% of reference with a coverageData >= 7X There is a 2.5% of reference with a coverageData >= 8X There is a 2.12% of reference with a coverageData >= 9X There is a 1.82% of reference with a coverageData >= 10X There is a 1.57% of reference with a coverageData >= 11X There is a 1.36% of reference with a coverageData >= 12X There is a 1.19% of reference with a coverageData >= 13X There is a 1.04% of reference with a coverageData >= 14X There is a 0.92% of reference with a coverageData >= 15X There is a 0.81% of reference with a coverageData >= 16X There is a 0.72% of reference with a coverageData >= 17X There is a 0.64% of reference with a coverageData >= 18X There is a 0.57% of reference with a coverageData >= 19X There is a 0.51% of reference with a coverageData >= 20X There is a 0.46% of reference with a coverageData >= 21X There is a 0.41% of reference with a coverageData >= 22X There is a 0.37% of reference with a coverageData >= 23X There is a 0.34% of reference with a coverageData >= 24X There is a 0.3% of reference with a coverageData >= 25X There is a 0.28% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.15% of reference with a coverageData >= 33X There is a 0.14% of reference with a coverageData >= 34X There is a 0.13% 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 0.1% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.08% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 217859063 0.8740562495930552 10.631435431949615 chr2 243199373 201790449 0.829732603792527 5.857153529245625 chr3 198022430 142302034 0.7186157345912784 3.0202677517894227 chr4 191154276 117437476 0.6143596599429457 5.457064835590625 chr5 180915260 128551543 0.7105621880652854 3.082035524489905 chr6 171115067 115945663 0.6775888589635418 3.1720560348053612 chr7 159138663 113278770 0.7118243163824997 3.424029962141331 chr8 146364022 114674003 0.7834849127062113 4.740574153645088 chr9 141213431 98040773 0.6942737125337604 3.9221322606037283 chr10 135534747 109092811 0.8049065897470558 3.375866541193485 chr11 135006516 110391227 0.8176733262267134 3.6797416003027346 chr12 133851895 101693257 0.7597446192300826 3.5622423397319904 chr13 115169878 66519292 0.5775754316593094 3.761077797577621 chr14 107349540 68402407 0.6371932939815113 3.1140016810472164 chr15 102531392 80188530 0.7820875971331784 5.348994974439547 chr16 90354753 81897085 0.9063948744345525 9.416937362881267 chr17 81195210 71050487 0.8750576173151101 3.5979263779820005 chr18 78077248 56195740 0.7197453988132368 3.617175316509105 chr19 59128983 47652742 0.805911747205258 3.882265064785979 chr20 63025520 67672204 1.0737270235929826 4.664777598110131 chr21 48129895 28988404 0.6022951847287429 4.266868631171166 chr22 51304566 38953110 0.7592523051457057 3.5692024036067234 chrMT 16571 26286 1.5862651620300525 7.692201350506416 chrX 155270560 4857666 0.03128517086561677 0.9203106937807596 chrY 59373566 22018329 0.3708439712042898 3.2469711345506806