BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926985.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 = 29,274,098 number of mapped reads = 28,853,277 (98.56%) number of supplementary alignments = 337,216 (1.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,476,106 number of mapped paired reads (second in pair) = 14,377,171 number of mapped paired reads (both in pair) = 28,635,314 number of mapped paired reads (singletons) = 217,963 number of mapped bases = 2,758,447,163 bp number of sequenced bases = 2,756,417,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,056,370 duplication rate = 5.28% >>>>>>> Insert size mean insert size = 113,729.089 std insert size = 3,344,464.4537 median insert size = 175 >>>>>>> Mapping quality mean mapping quality = 53.4759 >>>>>>> ACTG content number of A's = 776,861,152 bp (28.18%) number of C's = 572,386,588 bp (20.77%) number of T's = 785,033,993 bp (28.48%) number of G's = 621,886,237 bp (22.56%) number of N's = 249,350 bp (0.01%) GC percentage = 43.33% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 24,906,980 number of insertions = 432,155 mapped reads with insertion percentage = 1.47% number of deletions = 1,417,304 mapped reads with deletion percentage = 4.79% homopolymer indels = 52.72% >>>>>>> Coverage mean coverageData = 0.8911X std coverageData = 4.2771X There is a 32.81% of reference with a coverageData >= 1X There is a 19.22% of reference with a coverageData >= 2X There is a 11.44% of reference with a coverageData >= 3X There is a 7.3% of reference with a coverageData >= 4X There is a 4.79% of reference with a coverageData >= 5X There is a 3.25% of reference with a coverageData >= 6X There is a 2.25% of reference with a coverageData >= 7X There is a 1.59% of reference with a coverageData >= 8X There is a 1.14% of reference with a coverageData >= 9X There is a 0.83% of reference with a coverageData >= 10X There is a 0.61% of reference with a coverageData >= 11X There is a 0.46% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 234112960 0.9392673087863641 4.233147036318085 chr2 243199373 230401401 0.9473766241987803 5.6371925353687935 chr3 198022430 181367433 0.9158933813709892 1.9230383392583166 chr4 191154276 152736707 0.7990232298020893 2.6516107562262983 chr5 180915260 155200230 0.8578614650859192 1.8115046469303038 chr6 171115067 152694741 0.892351232869517 3.003392988157367 chr7 159138663 138969632 0.8732612765510038 2.4864979774181837 chr8 146364022 138764733 0.9480795287246205 2.324674889790842 chr9 141213431 120257094 0.8515981316253126 4.0437794224256605 chr10 135534747 135265202 0.9980112479938447 4.735723982875334 chr11 135006516 136517229 1.011189926566211 4.717492184381817 chr12 133851895 121167420 0.9052349987275115 2.199807771729113 chr13 115169878 80538998 0.6993060980754012 1.711233133733125 chr14 107349540 79090538 0.7367571207105312 1.7552408121587153 chr15 102531392 88620884 0.8643292778079127 2.027757178272728 chr16 90354753 89355935 0.9889455953689564 4.757338596874615 chr17 81195210 79639573 0.9808407786616969 2.689419032302231 chr18 78077248 73156058 0.9369702425987145 4.271600676532751 chr19 59128983 55140657 0.9325487130397626 2.9635512609880514 chr20 63025520 70417090 1.1172790006333941 2.3824115886524675 chr21 48129895 36044474 0.7488999092975375 3.1865611277906853 chr22 51304566 42413587 0.8267019937367758 2.115660147375531 chrMT 16571 15358552 926.8331422364372 660.8766224109789 chrX 155270560 146562513 0.9439169472950958 2.4360828632777585 chrY 59373566 4653522 0.07837700029673138 2.2055915232153507