BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630576.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 = 34,315,180 number of mapped reads = 33,887,777 (98.75%) number of supplementary alignments = 57,305 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,012,251 number of mapped paired reads (second in pair) = 16,875,526 number of mapped paired reads (both in pair) = 33,696,938 number of mapped paired reads (singletons) = 190,839 number of mapped bases = 3,322,928,472 bp number of sequenced bases = 3,320,420,396 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,434,188 duplication rate = 11.05% >>>>>>> Insert size mean insert size = 30,001.0266 std insert size = 1,741,192.7469 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 54.0542 >>>>>>> ACTG content number of A's = 953,961,097 bp (28.73%) number of C's = 685,869,438 bp (20.66%) number of T's = 959,920,152 bp (28.91%) number of G's = 720,166,541 bp (21.69%) number of N's = 503,168 bp (0.02%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 29,189,393 number of insertions = 627,636 mapped reads with insertion percentage = 1.82% number of deletions = 1,856,858 mapped reads with deletion percentage = 5.32% homopolymer indels = 54.49% >>>>>>> Coverage mean coverageData = 1.0734X std coverageData = 5.1571X There is a 16.72% of reference with a coverageData >= 1X There is a 11.86% of reference with a coverageData >= 2X There is a 9.02% of reference with a coverageData >= 3X There is a 7.26% of reference with a coverageData >= 4X There is a 6.02% of reference with a coverageData >= 5X There is a 5.11% of reference with a coverageData >= 6X There is a 4.4% of reference with a coverageData >= 7X There is a 3.84% of reference with a coverageData >= 8X There is a 3.38% of reference with a coverageData >= 9X There is a 3% of reference with a coverageData >= 10X There is a 2.68% of reference with a coverageData >= 11X There is a 2.41% of reference with a coverageData >= 12X There is a 2.18% of reference with a coverageData >= 13X There is a 1.97% of reference with a coverageData >= 14X There is a 1.8% of reference with a coverageData >= 15X There is a 1.64% of reference with a coverageData >= 16X There is a 1.5% of reference with a coverageData >= 17X There is a 1.38% of reference with a coverageData >= 18X There is a 1.27% of reference with a coverageData >= 19X There is a 1.17% of reference with a coverageData >= 20X There is a 1.08% of reference with a coverageData >= 21X There is a 1% of reference with a coverageData >= 22X There is a 0.93% of reference with a coverageData >= 23X There is a 0.86% of reference with a coverageData >= 24X There is a 0.8% of reference with a coverageData >= 25X There is a 0.75% of reference with a coverageData >= 26X There is a 0.7% of reference with a coverageData >= 27X There is a 0.65% of reference with a coverageData >= 28X There is a 0.61% of reference with a coverageData >= 29X There is a 0.57% of reference with a coverageData >= 30X There is a 0.53% of reference with a coverageData >= 31X There is a 0.5% of reference with a coverageData >= 32X There is a 0.47% of reference with a coverageData >= 33X There is a 0.44% of reference with a coverageData >= 34X There is a 0.41% of reference with a coverageData >= 35X There is a 0.39% of reference with a coverageData >= 36X There is a 0.37% of reference with a coverageData >= 37X There is a 0.35% of reference with a coverageData >= 38X There is a 0.33% of reference with a coverageData >= 39X There is a 0.31% of reference with a coverageData >= 40X There is a 0.29% of reference with a coverageData >= 41X There is a 0.27% of reference with a coverageData >= 42X There is a 0.26% of reference with a coverageData >= 43X There is a 0.24% of reference with a coverageData >= 44X There is a 0.23% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 287673298 1.1541527834347902 5.635524071547698 chr2 243199373 281415947 1.157140923221048 6.070548974489014 chr3 198022430 217708385 1.0994127533936433 4.744539472297759 chr4 191154276 179269388 0.9378256754245978 4.557540816610583 chr5 180915260 196175204 1.0843485729175084 4.688252257639591 chr6 171115067 180775896 1.0564580850148046 4.751772671555121 chr7 159138663 166814808 1.0482355755370396 4.676504663589058 chr8 146364022 164435888 1.1234720510755027 5.011147234734597 chr9 141213431 144467789 1.0230456690766192 5.196464776396764 chr10 135534747 160925984 1.1873411620416423 5.1287334547046575 chr11 135006516 166793069 1.2354445840228927 5.526485487644332 chr12 133851895 149936601 1.1201679363598103 5.024364930247262 chr13 115169878 96176196 0.8350811659277785 4.134384775183826 chr14 107349540 103447631 0.9636522988361198 4.5096605585950975 chr15 102531392 104179579 1.0160749500016542 4.761322349766756 chr16 90354753 108740896 1.2034883876003735 7.365467926473621 chr17 81195210 94381269 1.1623994691312456 5.329381481390342 chr18 78077248 87570473 1.1215875974522054 5.184582367270784 chr19 59128983 64129472 1.0845691697420197 5.413353806721166 chr20 63025520 86329449 1.369753855263709 6.001061903943209 chr21 48129895 44355598 0.9215810256806087 5.7919066269617945 chr22 51304566 48453217 0.9444230948177205 5.041370001654721 chrMT 16571 2658 0.16040070001810391 0.9177434702070689 chrX 155270560 184058965 1.185408006514564 5.044085503321731 chrY 59373566 4710812 0.07934190781129771 2.6051784169530707