BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618592.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 = 57,902,748 number of mapped reads = 53,967,348 (93.2%) number of supplementary alignments = 183,733 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,543,735 number of mapped paired reads (second in pair) = 26,423,613 number of mapped paired reads (both in pair) = 51,730,264 number of mapped paired reads (singletons) = 2,237,084 number of mapped bases = 5,072,454,791 bp number of sequenced bases = 5,068,963,101 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,340,527 duplication rate = 27.84% >>>>>>> Insert size mean insert size = 94,746.7609 std insert size = 3,075,349.0195 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 53.4834 >>>>>>> ACTG content number of A's = 1,387,897,141 bp (27.38%) number of C's = 1,108,879,133 bp (21.88%) number of T's = 1,408,213,641 bp (27.78%) number of G's = 1,162,406,921 bp (22.93%) number of N's = 1,566,265 bp (0.03%) GC percentage = 44.81% >>>>>>> Mismatches and indels general error rate = 0.0142 number of mismatches = 70,463,792 number of insertions = 941,748 mapped reads with insertion percentage = 1.72% number of deletions = 2,555,283 mapped reads with deletion percentage = 4.62% homopolymer indels = 52.6% >>>>>>> Coverage mean coverageData = 1.6386X std coverageData = 7.1994X There is a 26.11% of reference with a coverageData >= 1X There is a 18.35% of reference with a coverageData >= 2X There is a 14.2% of reference with a coverageData >= 3X There is a 11.52% of reference with a coverageData >= 4X There is a 9.56% of reference with a coverageData >= 5X There is a 8.09% of reference with a coverageData >= 6X There is a 6.94% of reference with a coverageData >= 7X There is a 6.01% of reference with a coverageData >= 8X There is a 5.25% of reference with a coverageData >= 9X There is a 4.63% of reference with a coverageData >= 10X There is a 4.1% of reference with a coverageData >= 11X There is a 3.65% of reference with a coverageData >= 12X There is a 3.27% of reference with a coverageData >= 13X There is a 2.94% of reference with a coverageData >= 14X There is a 2.65% of reference with a coverageData >= 15X There is a 2.4% of reference with a coverageData >= 16X There is a 2.19% of reference with a coverageData >= 17X There is a 1.99% of reference with a coverageData >= 18X There is a 1.82% of reference with a coverageData >= 19X There is a 1.67% of reference with a coverageData >= 20X There is a 1.53% of reference with a coverageData >= 21X There is a 1.41% of reference with a coverageData >= 22X There is a 1.3% of reference with a coverageData >= 23X There is a 1.2% of reference with a coverageData >= 24X There is a 1.11% of reference with a coverageData >= 25X There is a 1.03% of reference with a coverageData >= 26X There is a 0.96% of reference with a coverageData >= 27X There is a 0.89% of reference with a coverageData >= 28X There is a 0.83% of reference with a coverageData >= 29X There is a 0.77% of reference with a coverageData >= 30X There is a 0.72% of reference with a coverageData >= 31X There is a 0.67% of reference with a coverageData >= 32X There is a 0.63% of reference with a coverageData >= 33X There is a 0.59% of reference with a coverageData >= 34X There is a 0.55% of reference with a coverageData >= 35X There is a 0.52% of reference with a coverageData >= 36X There is a 0.49% of reference with a coverageData >= 37X There is a 0.46% of reference with a coverageData >= 38X There is a 0.43% of reference with a coverageData >= 39X There is a 0.41% of reference with a coverageData >= 40X There is a 0.38% of reference with a coverageData >= 41X There is a 0.36% of reference with a coverageData >= 42X There is a 0.34% of reference with a coverageData >= 43X There is a 0.32% of reference with a coverageData >= 44X There is a 0.31% of reference with a coverageData >= 45X There is a 0.29% of reference with a coverageData >= 46X There is a 0.27% of reference with a coverageData >= 47X There is a 0.26% of reference with a coverageData >= 48X There is a 0.25% of reference with a coverageData >= 49X There is a 0.23% of reference with a coverageData >= 50X There is a 0.22% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 438413819 1.7589276898932982 7.946696600027764 chr2 243199373 428484285 1.7618642668128919 8.21156289145998 chr3 198022430 324538509 1.6388977198189114 5.699533089269846 chr4 191154276 261830353 1.3697331730104745 6.115203994721987 chr5 180915260 293268822 1.6210286628115285 7.366481904751397 chr6 171115067 271354980 1.5858041302698376 5.966089813253345 chr7 159138663 258631991 1.6251989687760542 6.214205133680539 chr8 146364022 246686654 1.6854323257118473 6.383325269118841 chr9 141213431 215926475 1.5290788806059106 8.227459170748359 chr10 135534747 248620850 1.8343698239979744 6.416365898526646 chr11 135006516 261107537 1.9340365542060207 7.4851330145774195 chr12 133851895 223452053 1.6693977548842323 6.985192381946293 chr13 115169878 139395438 1.2103463198945128 4.9968297365706515 chr14 107349540 154823543 1.4422376006455175 5.988977962611538 chr15 102531392 166027830 1.6192877787126894 7.179720307099926 chr16 90354753 178537567 1.975962094655939 12.577224906638643 chr17 81195210 162932679 2.006678460465833 8.193067276026456 chr18 78077248 126417121 1.6191288017733412 8.042577236583 chr19 59128983 105405101 1.7826300344113817 7.410183111682352 chr20 63025520 138037594 2.1901857215934117 7.3883460733805375 chr21 48129895 66305682 1.3776402794978049 9.687350961764661 chr22 51304566 87190013 1.6994591280627926 7.105912565901577 chrMT 16571 13265 0.800494840383803 3.474488164468249 chrX 155270560 265999173 1.7131333396363098 5.916796161429813 chrY 59373566 9053457 0.15248295849368387 4.507781752120889