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	1,196,232	C→T	41.8%	T370T (ACC→ACT)	icd →	isocitrate dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,196,232	0	C	T	41.8%	22.3 / 42.7	43	T370T (ACC→ACT)	icd	isocitrate dehydrogenase
Reads supporting (aligned to +/- strand): ref base C (11/14); new base T (11/7); total (22/21)
Fisher's exact test for biased strand distribution p-value = 3.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.16e-01

CCCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAAT  >  NC_000913/1196091‑1196374

cccTGGTGCGAACATCGGGGACGGATGCGCCGGGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCg                                                                                                                                               <  1:516368/143‑1 (MQ=255)

    ggTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACACAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGc                                                                                                                                           <  2:301323/143‑1 (MQ=255)

    ggTGCAAACATCGGTCACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGc                                                                                                                                           <  2:774846/143‑1 (MQ=255)

          atcgtCGGTGACGAATGCGCCCTTTTTGAAGCTACCTACTGTATTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGa                                                                                                                                     <  1:306596/139‑1 (MQ=38)

          aaCATCGGTGACGAATGCGCCCTGGTTGAAGCCACCCACGGTACTGCGCCGAAATAGGCCGGTCAGGACAAAGTAAGTCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGa                                                                                                                                     <  2:581643/143‑1 (MQ=255)

            cATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGAcc                                                                                                                                   <  2:291593/143‑2 (MQ=255)

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

                                                                            gACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                                                   >  2:981290/1‑143 (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)

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

CCCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAAT  >  NC_000913/1196091‑1196374

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