BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618591.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 = 60,596,386 number of mapped reads = 57,529,088 (94.94%) number of supplementary alignments = 260,892 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 29,332,381 number of mapped paired reads (second in pair) = 28,196,707 number of mapped paired reads (both in pair) = 55,606,600 number of mapped paired reads (singletons) = 1,922,488 number of mapped bases = 5,374,663,375 bp number of sequenced bases = 5,371,036,064 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,948,302 duplication rate = 26.96% >>>>>>> Insert size mean insert size = 104,919.6654 std insert size = 3,241,418.592 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.2764 >>>>>>> ACTG content number of A's = 1,464,336,129 bp (27.26%) number of C's = 1,166,237,970 bp (21.71%) number of T's = 1,494,075,147 bp (27.82%) number of G's = 1,244,067,365 bp (23.16%) number of N's = 2,319,453 bp (0.04%) GC percentage = 44.88% >>>>>>> Mismatches and indels general error rate = 0.0129 number of mismatches = 67,799,800 number of insertions = 974,680 mapped reads with insertion percentage = 1.67% number of deletions = 2,620,287 mapped reads with deletion percentage = 4.44% homopolymer indels = 52.34% >>>>>>> Coverage mean coverageData = 1.7362X std coverageData = 6.6265X There is a 31.32% of reference with a coverageData >= 1X There is a 22.36% of reference with a coverageData >= 2X There is a 16.91% of reference with a coverageData >= 3X There is a 13.5% of reference with a coverageData >= 4X There is a 10.95% of reference with a coverageData >= 5X There is a 9.1% of reference with a coverageData >= 6X There is a 7.63% of reference with a coverageData >= 7X There is a 6.49% of reference with a coverageData >= 8X There is a 5.56% of reference with a coverageData >= 9X There is a 4.81% of reference with a coverageData >= 10X There is a 4.19% of reference with a coverageData >= 11X There is a 3.67% of reference with a coverageData >= 12X There is a 3.22% of reference with a coverageData >= 13X There is a 2.85% of reference with a coverageData >= 14X There is a 2.53% of reference with a coverageData >= 15X There is a 2.26% of reference with a coverageData >= 16X There is a 2.02% of reference with a coverageData >= 17X There is a 1.81% of reference with a coverageData >= 18X There is a 1.63% of reference with a coverageData >= 19X There is a 1.47% of reference with a coverageData >= 20X There is a 1.33% of reference with a coverageData >= 21X There is a 1.21% of reference with a coverageData >= 22X There is a 1.1% of reference with a coverageData >= 23X There is a 1% of reference with a coverageData >= 24X There is a 0.91% of reference with a coverageData >= 25X There is a 0.83% of reference with a coverageData >= 26X There is a 0.76% of reference with a coverageData >= 27X There is a 0.7% of reference with a coverageData >= 28X There is a 0.64% of reference with a coverageData >= 29X There is a 0.59% of reference with a coverageData >= 30X There is a 0.54% of reference with a coverageData >= 31X There is a 0.5% of reference with a coverageData >= 32X There is a 0.46% of reference with a coverageData >= 33X There is a 0.43% of reference with a coverageData >= 34X There is a 0.4% of reference with a coverageData >= 35X There is a 0.37% of reference with a coverageData >= 36X There is a 0.34% of reference with a coverageData >= 37X There is a 0.32% of reference with a coverageData >= 38X There is a 0.3% of reference with a coverageData >= 39X There is a 0.28% of reference with a coverageData >= 40X There is a 0.26% of reference with a coverageData >= 41X There is a 0.24% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 482651190 1.9364091774920793 8.144542132453081 chr2 243199373 448239273 1.843093867680325 7.881877403070004 chr3 198022430 340832290 1.7211802218566856 5.446555382297753 chr4 191154276 283401082 1.4825777792174526 5.431986217682842 chr5 180915260 301891259 1.6686887496389193 5.571013992450146 chr6 171115067 297388558 1.7379448999660563 5.752632055921184 chr7 159138663 278700318 1.7513048856015587 5.585234156101533 chr8 146364022 259687876 1.7742603165141226 5.681463623247674 chr9 141213431 235000096 1.6641483344456094 7.161262756666742 chr10 135534747 263255847 1.9423494921195374 5.721329906552748 chr11 135006516 265673512 1.9678569588448604 7.770046764335017 chr12 133851895 249365174 1.8629932284485027 6.180385256097704 chr13 115169878 145355690 1.2620981503514312 4.320049938731049 chr14 107349540 157974519 1.4715900878569206 5.103770964165376 chr15 102531392 169062325 1.6488835438808829 5.581021460649282 chr16 90354753 182625982 2.0212105720658657 12.943882691773318 chr17 81195210 167937846 2.0683220845170545 6.76598394572168 chr18 78077248 129314248 1.6562347074528037 6.448533358026812 chr19 59128983 114837326 1.9421495208195954 7.014295865792449 chr20 63025520 148166602 2.350898524914987 6.543223749090696 chr21 48129895 71542862 1.486453731095819 7.7290745945527695 chr22 51304566 89453424 1.7435762735036098 6.223350968400285 chrMT 16571 14569 0.8791865306861384 2.3144327128143063 chrX 155270560 283974116 1.8288986398967066 5.391309115786515 chrY 59373566 8317391 0.14008575802908654 4.801973161000282