BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975287.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 39,573,016 number of mapped reads = 39,349,380 (99.43%) number of supplementary alignments = 93,473 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 19,734,995 number of mapped paired reads (second in pair) = 19,614,385 number of mapped paired reads (both in pair) = 39,170,564 number of mapped paired reads (singletons) = 178,816 number of mapped bases = 3,679,412,210 bp number of sequenced bases = 3,678,126,726 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,644,941 duplication rate = 60.03% >>>>>>> Insert size mean insert size = 107,499.1161 std insert size = 3,222,762.7442 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 56.2047 >>>>>>> ACTG content number of A's = 1,020,387,599 bp (27.74%) number of C's = 789,595,711 bp (21.47%) number of T's = 1,032,635,966 bp (28.08%) number of G's = 834,756,080 bp (22.7%) number of N's = 751,370 bp (0.02%) GC percentage = 44.16% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 28,748,643 number of insertions = 394,353 mapped reads with insertion percentage = 0.99% number of deletions = 857,993 mapped reads with deletion percentage = 2.15% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 1.1886X std coverageData = 16.7265X There is a 7.23% of reference with a coverageData >= 1X There is a 4.84% of reference with a coverageData >= 2X There is a 2.97% of reference with a coverageData >= 3X There is a 2.47% of reference with a coverageData >= 4X There is a 2.11% of reference with a coverageData >= 5X There is a 1.93% of reference with a coverageData >= 6X There is a 1.79% of reference with a coverageData >= 7X There is a 1.69% of reference with a coverageData >= 8X There is a 1.6% of reference with a coverageData >= 9X There is a 1.53% of reference with a coverageData >= 10X There is a 1.46% of reference with a coverageData >= 11X There is a 1.4% of reference with a coverageData >= 12X There is a 1.35% of reference with a coverageData >= 13X There is a 1.3% of reference with a coverageData >= 14X There is a 1.25% of reference with a coverageData >= 15X There is a 1.21% of reference with a coverageData >= 16X There is a 1.17% of reference with a coverageData >= 17X There is a 1.13% of reference with a coverageData >= 18X There is a 1.1% of reference with a coverageData >= 19X There is a 1.07% of reference with a coverageData >= 20X There is a 1.04% of reference with a coverageData >= 21X There is a 1.01% of reference with a coverageData >= 22X There is a 0.98% of reference with a coverageData >= 23X There is a 0.95% of reference with a coverageData >= 24X There is a 0.93% of reference with a coverageData >= 25X There is a 0.91% of reference with a coverageData >= 26X There is a 0.88% of reference with a coverageData >= 27X There is a 0.86% of reference with a coverageData >= 28X There is a 0.84% of reference with a coverageData >= 29X There is a 0.82% of reference with a coverageData >= 30X There is a 0.81% of reference with a coverageData >= 31X There is a 0.79% of reference with a coverageData >= 32X There is a 0.77% of reference with a coverageData >= 33X There is a 0.75% of reference with a coverageData >= 34X There is a 0.74% of reference with a coverageData >= 35X There is a 0.72% of reference with a coverageData >= 36X There is a 0.71% of reference with a coverageData >= 37X There is a 0.69% of reference with a coverageData >= 38X There is a 0.68% of reference with a coverageData >= 39X There is a 0.67% of reference with a coverageData >= 40X There is a 0.65% of reference with a coverageData >= 41X There is a 0.64% of reference with a coverageData >= 42X There is a 0.63% of reference with a coverageData >= 43X There is a 0.62% of reference with a coverageData >= 44X There is a 0.61% of reference with a coverageData >= 45X There is a 0.6% of reference with a coverageData >= 46X There is a 0.58% of reference with a coverageData >= 47X There is a 0.57% of reference with a coverageData >= 48X There is a 0.56% of reference with a coverageData >= 49X There is a 0.55% of reference with a coverageData >= 50X There is a 0.54% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 442481522 1.7752474205470485 21.715036295587513 chr2 243199373 277542738 1.1412148583129775 14.879607338948887 chr3 198022430 184820251 0.9333298808624861 13.192397038225511 chr4 191154276 181551946 0.949766595856846 14.067029019840815 chr5 180915260 177201767 0.9794738542232424 12.905599547584838 chr6 171115067 363065997 2.121765215450022 29.14261076592988 chr7 159138663 198096989 1.2448074230710358 18.58570884835177 chr8 146364022 129800979 0.8868366503347387 12.727713822425219 chr9 141213431 150114823 1.063035023913554 14.381068271062453 chr10 135534747 159151261 1.1742469331499177 14.820450138553605 chr11 135006516 153796701 1.1391798378087172 14.681014154292388 chr12 133851895 214432642 1.6020142411879936 19.28637320096661 chr13 115169878 73625234 0.6392750889255956 11.806086000030637 chr14 107349540 122084919 1.1372654135266904 15.942897752518956 chr15 102531392 129606748 1.2640689399788896 16.659702175585952 chr16 90354753 103054914 1.1405588591449085 14.378530565620292 chr17 81195210 132466181 1.6314531485293282 17.931732268144952 chr18 78077248 69090862 0.8849039095230405 12.811989344859501 chr19 59128983 139237777 2.3548143386805758 25.97470175492526 chr20 63025520 82370248 1.3069348416324054 19.3000466690538 chr21 48129895 35532353 0.7382595162528404 12.471184396257579 chr22 51304566 53418437 1.0412023951240519 14.711813133835237 chrMT 16571 60788 3.668336250075433 10.935091251244236 chrX 155270560 98423752 0.633885470626241 10.45735007830867 chrY 59373566 8382381 0.1411803528863333 5.0572682585128