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
A3 F28 I1 R1	161	50.8	1735388	98.6%	1711092	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,195,548	A→G	K142K (AAA→AAG)	icd →	isocitrate dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,195,548	0	A	G	97.4%	128.7 / ‑4.2	39	K142K (AAA→AAG)	icd	isocitrate dehydrogenase
Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (20/18); total (21/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.21e-01

TTGCCATTAAAGGTCCGCTGACCACTCCGGTTGGTGGCGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAACACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGGGTGAAGAA  >  NC_000913/1195412‑1195682

ttGCCATTAAAGGTCCGCTGACCACTCCGGTTGGTGGCGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAgcac                                                                                                                                     <  1:855025/140‑1 (MQ=255)

   ccATTAAAGGTCCGCTGACCACTCCGGTTGGTGGCGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCt                                                                                                                                  >  2:524451/1‑140 (MQ=255)

   ccATTAAAGGTCCGCTGACCACTCCGGTTGGTGGCGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCt                                                                                                                                  >  2:217683/1‑140 (MQ=255)

        aaaGGTCCGCTGACCACTCCGGTTGGTGGCGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACt                                                                                                                             <  1:217683/140‑1 (MQ=255)

            gTCCGCTGACCACTCCGGTTGGTGGCGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGAcc                                                                                                                         <  1:11186/140‑1 (MQ=255)

             tCCGCTGACCACTCCGGTTGGTGGCGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCg                                                                                                                        <  1:816389/140‑1 (MQ=255)

             tCCGCTGACCACTCCGGTTGGTGGCGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCg                                                                                                                        >  1:59830/1‑140 (MQ=255)

             tCCGCTGACCACTCCGGTTGGTGGCGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCg                                                                                                                        <  2:819266/140‑1 (MQ=255)

              ccGCTGACCACTCCGGTTGGTGGCGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGa                                                                                                                       <  1:774999/140‑1 (MQ=255)

              ccGCTGACCACTCCGGTTGGTGGCGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGa                                                                                                                       <  1:447455/140‑1 (MQ=255)

                         tCCGGTTGGTGGCGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCt                                                                                                            >  2:230936/1‑140 (MQ=255)

                                       gTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCg                                                                                              <  2:33459/140‑1 (MQ=255)

                                                     aaCGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGc                                                                                >  1:592217/1‑140 (MQ=255)

                                                           gCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATg                                                                                 <  1:347000/133‑1 (MQ=255)

                                                           gCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATg                                                                                 >  2:347000/1‑133 (MQ=255)

                                                            accTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATc                                                                         <  1:21806/139‑1 (MQ=255)

                                                              cTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGa                                                                       <  1:524451/140‑1 (MQ=255)

                                                                            ggATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGAct                                                         <  2:592217/140‑1 (MQ=255)

                                                                                     cATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACg                                                >  1:383711/1‑140 (MQ=255)

                                                                                           cctgcGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCgaga                                          >  1:718437/1‑140 (MQ=255)

                                                                                           cctgcGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCgaga                                          <  2:59830/140‑1 (MQ=255)

                                                                                           cctgcGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCgaga                                          >  2:683748/1‑140 (MQ=255)

                                                                                           cctgcGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCgaga                                          >  1:308038/1‑140 (MQ=255)

                                                                                             tgcGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGaaa                                        >  1:636512/1‑140 (MQ=255)

                                                                                               cGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGt                                      >  2:145719/1‑140 (MQ=255)

                                                                                                              tATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTc                            <  1:339466/135‑1 (MQ=255)

                                                                                                              tATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTc                            >  2:339466/1‑135 (MQ=255)

                                                                                                              tATCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCg                       <  1:683748/140‑1 (MQ=255)

                                                                                                               aTCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTc                            >  1:468793/1‑134 (MQ=255)

                                                                                                               aTCAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTc                            <  2:468793/134‑1 (MQ=255)

                                                                                                                 cAGGGCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGa                    <  1:601819/140‑1 (MQ=255)

                                                                                                                   gggCACTCCAAGCCCGGTTAAACACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAag                  >  1:191630/1‑140 (MQ=255)

                                                                                                                    ggCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAaga                 >  2:623081/1‑140 (MQ=255)

                                                                                                                    ggCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAaga                 >  1:245741/1‑140 (MQ=255)

                                                                                                                     gCACTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAagag                >  1:231019/1‑140 (MQ=255)

                                                                                                                        cTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCGt                      >  2:864640/1‑131 (MQ=255)

                                                                                                                        cTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCGt                      <  1:864640/131‑1 (MQ=255)

                                                                                                                        cTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATg             <  1:145719/140‑1 (MQ=255)

                                                                                                                        cTCCAAGCCCGGTTAAGCACCCTGAACTGACCGATATGGCTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATg             >  2:464224/1‑140 (MQ=255)

                                                                                                                                   gTTAAGCACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGGGTgaagaa  >  2:300200/1‑140 (MQ=255)

                                                                                                                                   gTTAAGCACCCTGAACTGACCGATATGATTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGGGTgaagaa  >  2:303491/1‑140 (MQ=255)

TTGCCATTAAAGGTCCGCTGACCACTCCGGTTGGTGGCGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAACACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGGGTGAAGAA  >  NC_000913/1195412‑1195682

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A