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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,020,061	T→C	37.5%	Y161C (TAT→TGT)	uidC ←	predicted outer membrane porin protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,020,061	0	T	C	37.5%	23.1 / 28.4	48	Y161C (TAT→TGT)	uidC	predicted outer membrane porin protein
Reads supporting (aligned to +/- strand): ref base T (9/21); new base C (15/3); total (24/24)
Fisher's exact test for biased strand distribution p-value = 7.82e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.76e-01

AGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGCCATTAACGGAATACGA  >  minE/1019997‑1020129

aGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAAc                                                                   >  1:1324688/1‑68 (MQ=255)

    cATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAAt                                                              >  1:1045692/1‑69 (MQ=255)

    cATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAAt                                                              >  1:2810701/1‑69 (MQ=255)

    cATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAAt                                                              >  1:57442/1‑69 (MQ=255)

    cATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAAt                                                              >  1:1721226/1‑69 (MQ=255)

              cTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCa                                                     >  1:2366328/1‑68 (MQ=255)

              cTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCa                                                     >  1:839718/1‑68 (MQ=255)

                 gTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTaa                                                               <  1:2445616/55‑1 (MQ=255)

                 gTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTaa                                                               <  1:1859870/55‑1 (MQ=255)

                 gTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTaa                                                               <  1:184018/55‑1 (MQ=255)

                             ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg                                     <  1:1747893/69‑1 (MQ=255)

                             ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg                                     <  1:2685249/69‑1 (MQ=255)

                             ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg                                     <  1:1824142/69‑1 (MQ=255)

                             ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg                                     <  1:580172/69‑1 (MQ=255)

                             ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg                                     <  1:1565901/69‑1 (MQ=255)

                             ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg                                     <  1:1509602/69‑1 (MQ=255)

                             ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg                                     <  1:704601/69‑1 (MQ=255)

                             ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg                                     <  1:816/69‑1 (MQ=255)

                             ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg                                     <  1:915501/69‑1 (MQ=255)

                             ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg                                     <  1:109325/69‑1 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCt                                                        >  1:3366341/1‑48 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa                                   >  1:962575/1‑69 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa                                   >  1:487356/1‑69 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa                                   >  1:686073/1‑69 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa                                   >  1:3146949/1‑69 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa                                   >  1:2417925/1‑69 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa                                   >  1:2245930/1‑69 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa                                   >  1:1292686/1‑69 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa                                   >  1:2038991/1‑69 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa                                   >  1:1503713/1‑69 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa                                   >  1:2038235/1‑69 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa                                   >  1:1554046/1‑69 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa                                   >  1:1613192/1‑69 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa                                   >  1:1784359/1‑69 (MQ=255)

                               ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTACTTCAGAAACTGTCgg                                          >  1:1503286/1‑62 (MQ=255)

                                                tGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTgccagc                  <  1:880921/69‑1 (MQ=255)

                                                tGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTgccagc                  <  1:1757285/69‑1 (MQ=255)

                                                       aaaGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGCCATTaa            <  1:2202861/68‑1 (MQ=255)

                                                       aaaGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGCCATTaa            <  1:807776/68‑1 (MQ=255)

                                                       aaaGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGCCATTaa            <  1:3020599/68‑1 (MQ=255)

                                                       aaaGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGCCATTaa            <  1:2706933/68‑1 (MQ=255)

                                                       aaaGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGCCATTaa            <  1:2649903/68‑1 (MQ=255)

                                                        aaGCCCAATAACCTAATGCTCCTTCAGAAACTGTCTGTAATGTACGTTGCGAACTGCCAGCCATTaa            <  1:2496343/67‑1 (MQ=255)

                                                          gCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGCCATTAACgg         <  1:1921553/68‑1 (MQ=255)

                                                          gCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGCCATTAACgg         <  1:2119668/68‑1 (MQ=255)

                                                           cccAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGCCATTAACGGaa       <  1:1908214/69‑1 (MQ=255)

                                                            ccAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGCCATTAACGGAAt      >  1:1428922/1‑69 (MQ=255)

                                                            ccAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGCCATTAACGGAAt      >  1:1424644/1‑69 (MQ=255)

                                                                tAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGCCATTAACGGAATACGa  <  1:311190/69‑1 (MQ=255)

                                                                tAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGCCATTAACGGAATACGa  <  1:2420410/69‑1 (MQ=255)

AGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGCCATTAACGGAATACGA  >  minE/1019997‑1020129

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