Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A6 F21 I0 R2	370	72.1	3738297	91.5%	3420541	62.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	780,667	T→C	58.1%	D125D (GAT→GAC)	ycgM →	predicted isomerase/hydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	780,667	0	T	C	58.1%	13.4 / 35.1	31	D125D (GAT→GAC)	ycgM	predicted isomerase/hydrolase
Reads supporting (aligned to +/- strand): ref base T (5/8); new base C (11/7); total (16/15)
Fisher's exact test for biased strand distribution p-value = 2.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGCGTGATGTTCAGGGAAAAATGAAGAAAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGATAACTCTTGTCCGCTTTCCGGGTTTATTCCCGCGGCGGAATTTACCGGCGACCCGCAAAATAC  >  minE/780602‑780729

ttGCGTGATGTTCAGGGAAAAATGAAGAAAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGATAAct                                                            <  1:1345569/70‑1 (MQ=255)

   cGTGATGTTCAGGGAAAAATGAAGAAAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGACAACTCtt                                                         <  1:545327/70‑1 (MQ=255)

   cGTGATGTTCAGGGAAAAATGAAGAAAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGACAACTCtt                                                         <  1:45630/70‑1 (MQ=255)

     tGATGTTCAGGGAAAAATGAAGAAAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGATAACTCTTGTc                                                      <  1:356161/71‑1 (MQ=255)

     tGATGTTCAGGGAAAAATGAAGAAAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGATAACTCTTGTc                                                      >  1:2001011/1‑71 (MQ=255)

       aTGTTCAGGGAAAAATGAAGAAAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGATAACTCTTGTcc                                                     <  1:3711554/70‑1 (MQ=255)

         gTTCAGGGAAAAATGAAGAAAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGACAACTCTTGTCCGCt                                                  >  1:1120275/1‑71 (MQ=255)

             aGGGAAAAATGAAGAAAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGACAACTCTTGTCCGCTTTcc                                              <  1:1458129/71‑1 (MQ=255)

                gAAAAATGAAGAAAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGACAACTCTTGTCCGCTTTCCggg                                           >  1:3737286/1‑71 (MQ=255)

                   aaaTGAAGAAAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGACAACTCTTGt                                                       >  1:2266411/1‑56 (MQ=255)

                     aTGAAGAAAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGACAACTCTTGTCCGCTTTCCGGGTTTAt                                      <  1:3622052/71‑1 (MQ=255)

                       gaagaaAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGATAACTCTTGTcc                                                     <  1:3230391/54‑1 (MQ=255)

                        aagaaAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGACAACTCTTGTCCGCTTTCCGGGTTTATTcc                                   <  1:1629600/71‑1 (MQ=255)

                           aaaGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGACAACTCTTGTCCGCTTTCCGGGTTTATTCCcgc                                >  1:3428958/1‑71 (MQ=255)

                             aGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGACAACTCTTGTCCGCTTTCCGGGTTTATTCCCgcgg                              <  1:2380165/71‑1 (MQ=255)

                                cGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGATAACTCTTGTCCGCTTTCCGGGTTTATTCCCGcggcgg                           <  1:2335409/71‑1 (MQ=255)

                                 gggCAGCCGTGGGAAAAGGCTAAAGCGTTTGACAACTCTTGTCCGCTTTCCGGGTTTATTCCCGcggcgg                           >  1:2341050/1‑70 (MQ=255)

                                    cAGCCGTGGGAAAAGGCTAAAGCGTTTGACAACTCTTGTCCGCTTTCCGGGTTTATTCCCGCGGCGGAAtt                       >  1:1543873/1‑71 (MQ=255)

                                      gCCGTGGGAAAAGGCTAAAGCGTTTGATAACTCTTGTCCGCTTTCCGGGTTTATTCCCGCGGCGGAATTTa                     <  1:732465/71‑1 (MQ=255)

                                      gCCGTGGGAAAAGGCTAAAGCGTTTGATAACTCTTGTCCGCTTTCCGGGTTTATTCCCGCGGCGGAATTTa                     <  1:371823/71‑1 (MQ=255)

                                      gCCGTGGGAAAAGGCTAAAGCGTTTGACAACTCTTGTCCGCTTTCCGGGTTTATTCCCGCGGCGGAATTTa                     >  1:2980566/1‑71 (MQ=255)

                                          tGGGAAAAGGCTAAAGCGTTTGATAACTCTTGTCCGCTTTCCGGGTTTATTCCCGCGGCGGAAttt                      >  1:1456720/1‑66 (MQ=255)

                                          tGGGAAAAGGCTAAAGCGTTTGATAACTCTTGTCCGCTTTCCGGGTTTATTCCCGCGGCGGAATTTa                     >  1:1718513/1‑67 (MQ=255)

                                          tGGGAAAAGGCTAAAGCGTTTGATAACTCTTGTCCGCTTTCCGGGTTTATTCCCGCGGCGGAATTTa                     >  1:672684/1‑67 (MQ=255)

                                            ggAAAAGGCTAAAGCGTTTGACAACTCTTGTCCGCtt                                                 >  1:356220/1‑37 (MQ=255)

                                               aaaGGCTAAAGCGTTTGACAACTCTTGTCCGCTTTCCGGGTTTATTCCCGCGGCGGAATTTACCGGCGAcc            >  1:398448/1‑71 (MQ=255)

                                                  gtcTAAAGCGTTTGATAACTCTTGTCCGCTTTCCGGGTTTATTc                                    >  1:2354668/3‑44 (MQ=255)

                                                       aaGCGTTTGATAACTCTTGTCCGCTTTCCGGGTTTATTCCCGCGGCGGAATTTACCGGCGACCCGCaaaa     <  1:1045229/70‑1 (MQ=255)

                                                        aGCGTTTGACAACTCTTGTCCGCTTTCCGGGTTTATTCCcgc                                >  1:2891699/1‑42 (MQ=255)

                                                         gCGTTTGACAACTCTTGTCCGCTTTCCGGGTTTATTCCCGCGGCGGAATTTACCGGCGACCCGCAAAATa   >  1:265807/1‑70 (MQ=255)

                                                         gCGTTTGACAACTCTTGTCCGCTTTCCGGGTTTATTCCCGCGGCGGAATTTACCGGCGACCCGCAAAATAc  <  1:2164621/71‑1 (MQ=255)

TTGCGTGATGTTCAGGGAAAAATGAAGAAAGCCGGGCAGCCGTGGGAAAAGGCTAAAGCGTTTGATAACTCTTGTCCGCTTTCCGGGTTTATTCCCGCGGCGGAATTTACCGGCGACCCGCAAAATAC  >  minE/780602‑780729

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A