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
A29 F71 I0 R1	83	59.3	2271602	90.4%	2053528	142.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,196,245	T→C	35.7%	L375L (TTA→CTA) ‡	icd →	isocitrate dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,196,245	0	T	C	35.7%	35.2 / 27.8	43	L375L (TTA→CTA) ‡	icd	isocitrate dehydrogenase
Reads supporting (aligned to +/- strand): ref base T (12/15); new base C (12/4); total (24/19)
Fisher's exact test for biased strand distribution p-value = 6.44e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.35e-01

TCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTT  >  NC_000913/1196105‑1196387

tCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAATTCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTa                                                                                                                                              <  1:495036/143‑1 (MQ=255)

   gTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAAtt                                                                                                                                           <  1:696507/143‑1 (MQ=255)

   gTGACGAATGCGCCCTGCTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAAtt                                                                                                                                           <  1:377162/143‑1 (MQ=255)

         aaTGCGCCCTGTTTGAAGCCTGCCATGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTaaa                                                                                                                                     <  1:1038553/143‑1 (MQ=37)

         aaTGCGCCCTGTGTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTaaa                                                                                                                                     <  2:458070/143‑1 (MQ=255)

         aaTGCGCCCGGGTTGAAGACACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTaaa                                                                                                                                     <  1:22080/143‑1 (MQ=255)

          aTGCGCCCTGTCTGGAGCCACCCACGTTAGTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAg                                                                                                                                    <  2:658206/143‑1 (MQ=37)

              gcCCTGTTTGAAGCCACCCACGGGCCTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTAt                                                                                                                                <  1:29991/143‑1 (MQ=37)

               cccTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCCCTATTATTCTCTCCGCTGAGATGATACTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGGTAAAGGTacg                                                                                                                               >  2:327072/1‑141 (MQ=37)

                  tGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGGCACATGGGTTGGACCGAAGCGGCTGACTTTATTATTAAAGGTATGGag                                                                                                                            >  1:517968/1‑142 (MQ=255)

                        aaGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCa                                                                                                                      <  1:623760/143‑1 (MQ=255)

                           ccacccacGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGACTGTTCAAGGTATGGAAGGCGCAATc                                                                                                                   >  2:624557/1‑143 (MQ=25)

                                   ggTACTGCGCCGGAATATGCCGGTCAGGACAAAGTACATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaatgccaa                                                                                                           <  2:945639/143‑7 (MQ=18)

                                        tGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGCAGCGGCATACCCGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCg                                                                                                      >  1:770375/1‑143 (MQ=18)

                                           gcCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTaa                                                                                                   >  2:423038/1‑143 (MQ=18)

                                           gcCGAAAGATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCGCCGCTGAGATGATGCGGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTaa                                                                                                   <  2:616843/143‑1 (MQ=255)

                                            ccGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAAc                                                                                                  >  1:461060/1‑143 (MQ=255)

                                             cGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTCAAGGTATGGAAGGCGCAGTCAATGCCCAGACCGTAAct                                                                                                 >  1:19350/1‑142 (MQ=18)

                                             cGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCCTAAct                                                                                                 >  2:957954/1‑142 (MQ=18)

                                             cGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCCGACCCAACTGCTCAAGGTATGGACGGCGCAATCAACGCGAAAACCCTAAcc                                                                                                 >  2:856588/1‑143 (MQ=255)

                                             cGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCGCTATTATTCTCTCCGCTGAGATGATGCTGCGACATATAGGTTGGACTGAAACGGCAGACCTGATTGTTAAAGGTATGAAAGGCGCAATCAATGCCAAGACCGTaaac                                                                                                 >  2:87809/1‑141 (MQ=18)

                                               aaaTATGCCGGTCAGGACAAAGTAAATCCTGGCGCTATTATTCTCTCCGCTGAGATGATGCGGCGCCATACGGGTTGGACTAAAACGGCTGACCTGATAGTTACAGGTAAGAACGGCGCAATAAATGCCAAGACCGAAACTTa                                                                                               >  2:285576/1‑143 (MQ=255)

                                                aaTATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGCTGCTGCGCCATATGGGTTGGACTGACGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAAcacat                                                                                              >  2:54267/1‑139 (MQ=17)

                                                    tGCCGGTCAGGACAAAGTGAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGGCACCTGGGTTGGACCAAAGCGGCTGACTTAATTGTTAAAGGTAGTGAAGCAGCAACCAACGCAACAACCGTAAcccctcact                                                                                          >  2:1082064/1‑136 (MQ=255)

                                                     gCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACtt                                                                                         >  1:335317/1‑143 (MQ=17)

                                                     gCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACtt                                                                                         >  2:44594/1‑143 (MQ=255)

                                                      ccGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc                                                                                        <  1:44594/143‑1 (MQ=255)

                                                              gACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                                                                >  2:981290/1‑143 (MQ=255)

                                                              gACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                                                                >  1:932292/1‑143 (MQ=255)

                                                                 aaaGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTgct                                                                             >  2:912936/1‑141 (MQ=14)

                                                                             ggCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGAACGAAGCGGCGGACTGAGTTGGTAACGGTAGGGAGGGCGCAATCGACGCGAAAGCCGTAACCAATGACTACGGGAGTCTAGTGGAGGgcgttgc                                                                 >  1:389101/1‑139 (MQ=255)

                                                                                tctATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGTACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGAATTCGAGCGACTGATGGATGGCGCTAAAct                                                              >  2:370592/1‑143 (MQ=255)

                                                                                   attattCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                                                           <  2:461060/143‑1 (MQ=255)

                                                                                      atgctctcCGCTGAGATGATGCGGCGCCGCGTGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaa                                                        <  2:694439/140‑1 (MQ=255)

                                                                                        tttctcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGGAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAAt                                                      <  2:131058/141‑1 (MQ=255)

                                                                                                            tgcGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGTCGCTAAACTGCTGAAATGTCCAGAAAGTGGTGAcgcg                                  >  1:1003491/1‑143 (MQ=18)

                                                                                                                ccACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgccggca                              >  2:909999/1‑138 (MQ=255)

                                                                                                                              cgcaaGCGGCTGACTTAACGGTGAAAGGCATGGAAGGCGCAATCACCGCGAAAACCGTACCCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTaa                <  1:629283/140‑1 (MQ=17)

                                                                                                                               cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACATAGAGCTTCTGATGGATGACGCTAAACTGCTGAAATATTCAGAGTTTGGTGACGCGATCATCGAAAACCTGTAAt               >  2:891477/1‑143 (MQ=18)

                                                                                                                                      gCTGACTTAATTGTTAAAGGTATGGAAAGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGACGGATGACTCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAGAACATGTAATGCCGTAg        >  2:74214/1‑143 (MQ=18)

                                                                                                                                         gACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCTTTCGTCTGTTGGATGGCGCTAAACTGCTGAAAATTTCATAGTTTGGTGGCGCGCTCATCGAATACATGTAATGCCGTAGttt     <  1:715341/143‑1 (MQ=18)

                                                                                                                                         gACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTACGACTGCGAGCGTCTGAGGGATGGCGCTAAACTGCTGAAATGCTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGttt     <  1:1082064/143‑1 (MQ=255)

                                                                                                                                         gACTTAATTGTTAAAGGTAGGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGCGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGttt     <  2:965871/143‑1 (MQ=255)

                                                                                                                                            ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTACTGCCGTAGgttgtt  >  2:902023/1‑143 (MQ=255)

                                                                                                                                            ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGtt  >  2:903274/1‑143 (MQ=255)

TCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTT  >  NC_000913/1196105‑1196387

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A