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
A4 F21 I0 R1	1009	73.8	4146436	87.4%	3623985	60.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,207,505	C→T	40.0%	intergenic (‑195/+235)	tldD ← / ← yhdP	predicted peptidase/conserved membrane protein, predicted transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,207,505	0	C	T	40.0%	14.5 / 25.3	25	intergenic (‑195/+235)	tldD/yhdP	predicted peptidase/conserved membrane protein, predicted transporter
Reads supporting (aligned to +/- strand): ref base C (5/10); new base T (8/2); total (13/12)
Fisher's exact test for biased strand distribution p-value = 4.14e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.08e-01

AGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGCCGGATGCGGCGTAAACGCCTTATCCGACCTACG  >  minE/2207439‑2207575

aGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCTTGa                                                                     >  1:1614873/1‑70 (MQ=25)

aGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCTTGa                                                                     >  1:4043798/1‑70 (MQ=25)

  gCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCTTGAt                                                                    >  1:2862310/1‑69 (MQ=25)

  gCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATaa                                                                  <  1:4100797/71‑1 (MQ=34)

  gCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATaa                                                                  <  1:3469321/71‑1 (MQ=34)

    aaCGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATAAGa                                                                >  1:1708206/1‑71 (MQ=34)

     aCGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCTTGATAAGAc                                                               >  1:584347/1‑71 (MQ=21)

     aCGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATaa                                                                  <  1:2445288/68‑1 (MQ=35)

     aCGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATaa                                                                  <  1:3979269/68‑1 (MQ=35)

     aCGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCAGTTTGTAGGCCTGATaa                                                                  <  1:1768426/68‑1 (MQ=25)

      cGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCTTGATAAGACg                                                              <  1:2427468/71‑1 (MQ=21)

       ggCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATAAGACg                                                              >  1:746819/1‑70 (MQ=35)

       ggCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATAAGACg                                                              >  1:1933848/1‑70 (MQ=35)

          tGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCTTGATAAGACGca                                                            >  1:3829605/1‑69 (MQ=25)

           gTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGGTA‑GTGCGTTTTGTAGGCCTGATAAGACGcg                                                            >  1:2815202/1‑66 (MQ=11)

            tCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCTTGATAAGACGCACAGc                                                        >  1:798470/1‑71 (MQ=14)

            tCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCTTGATAAGACGCACAGc                                                        >  1:3687484/1‑71 (MQ=14)

            tCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATAAGACGcaca                                                          <  1:415437/69‑1 (MQ=31)

                                              gTTATGTTCCGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGCCGTATGCGGCGTa                      <  1:3862741/71‑1 (MQ=14)

                                              gTTATGTTCCGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGCCGGAAGCGGCGTa                      <  1:3032148/71‑1 (MQ=14)

                                                 aTGTTCCGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGCCGGATGCGGCGTAAAc                   >  1:1883524/1‑71 (MQ=34)

                                                  tGTTCCGTTTGTAGGCTTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGCCGGATGCGGCGTAAACg                  >  1:2789144/1‑71 (MQ=21)

                                                       cGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGCCGGATGCGGCGTAAACGCCtt              <  1:2923824/70‑1 (MQ=37)

                                                       cGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGCCGGATGCGGCGTAAACGCCtt              <  1:2792355/70‑1 (MQ=37)

                                                         tttGTAGGCTTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGCCGGATGCGGCGTAAACg                  <  1:1087958/64‑1 (MQ=25)

                                                                  cTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGCCGGATGCGGCGTAAACGCCTTATCCGACCTACg  >  1:3226532/1‑71 (MQ=34)

AGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGCCGGATGCGGCGTAAACGCCTTATCCGACCTACG  >  minE/2207439‑2207575

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