BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926976.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 21,175,238 number of mapped reads = 20,647,297 (97.51%) number of supplementary alignments = 943,004 (4.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,375,414 number of mapped paired reads (second in pair) = 10,271,883 number of mapped paired reads (both in pair) = 20,311,232 number of mapped paired reads (singletons) = 336,065 number of mapped bases = 1,846,314,739 bp number of sequenced bases = 1,844,846,165 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,117,244 duplication rate = 8.24% >>>>>>> Insert size mean insert size = 473,776.1174 std insert size = 6,751,376.6968 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 52.0994 >>>>>>> ACTG content number of A's = 527,955,464 bp (28.62%) number of C's = 354,731,130 bp (19.23%) number of T's = 541,798,365 bp (29.37%) number of G's = 420,230,425 bp (22.78%) number of N's = 130,781 bp (0.01%) GC percentage = 42.01% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 18,108,647 number of insertions = 335,481 mapped reads with insertion percentage = 1.6% number of deletions = 986,484 mapped reads with deletion percentage = 4.65% homopolymer indels = 51.47% >>>>>>> Coverage mean coverageData = 0.5964X std coverageData = 2.3851X There is a 27.69% of reference with a coverageData >= 1X There is a 13.86% of reference with a coverageData >= 2X There is a 6.93% of reference with a coverageData >= 3X There is a 3.87% of reference with a coverageData >= 4X There is a 2.24% of reference with a coverageData >= 5X There is a 1.37% of reference with a coverageData >= 6X There is a 0.86% of reference with a coverageData >= 7X There is a 0.56% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 150694147 0.6045888527595684 2.624267539663477 chr2 243199373 163111874 0.6706920005093928 4.235485275519561 chr3 198022430 127407151 0.6433975736991007 1.4080641647100478 chr4 191154276 117122520 0.612712006505154 2.1546827217392077 chr5 180915260 112404300 0.6213091145545158 1.3737476908894075 chr6 171115067 106205267 0.6206657827507381 1.9360496062387529 chr7 159138663 95416962 0.5995837856197146 2.11309212733376 chr8 146364022 95194251 0.6503937900804612 1.6897474576081417 chr9 141213431 77915189 0.55175480439959 2.9162775863123405 chr10 135534747 86477661 0.6380479022106412 2.9065440441114467 chr11 135006516 86635719 0.6417150932181673 2.176323221353972 chr12 133851895 84332181 0.6300409941898842 1.8178990508719197 chr13 115169878 56611464 0.4915474860536016 1.2947773778137843 chr14 107349540 56090949 0.5225075859663675 1.3699643679863027 chr15 102531392 52698435 0.513973661842024 1.3686378399341765 chr16 90354753 56345460 0.6236026122499609 4.426620846756674 chr17 81195210 46119610 0.5680089995456629 2.058878243825429 chr18 78077248 48544141 0.621745031279791 2.9996391413556176 chr19 59128983 27753789 0.4693770735072511 1.8161999343578776 chr20 63025520 41347744 0.6560476454617113 1.5314885474289497 chr21 48129895 23147164 0.48093111360413315 1.828310838842116 chr22 51304566 20648364 0.40246640035898557 1.1974512368280241 chrMT 16571 216001 13.034880212419287 12.280199009154739 chrX 155270560 110207511 0.7097772494669949 1.6920525343908468 chrY 59373566 3666885 0.061759554748657006 2.060963655595757