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	2,051,274	A→G	38.8%	G135G (GGT→GGC)	ygiF ←	predicted adenylate cyclase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,051,274	0	A	G	38.8%	22.3 / 33.8	54	G135G (GGT→GGC)	ygiF	predicted adenylate cyclase
Reads supporting (aligned to +/- strand): ref base A (21/12); new base G (17/4); total (38/16)
Fisher's exact test for biased strand distribution p-value = 2.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.70e-01

ACAGATAGGTTCAGCAAATTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCGACCGCCACCAGCCATTTTTCGCGATAAAAATCGGTGCTGAACAGCGGCTGCACGC  >  minE/2051208‑2051335

acaGATAGGTTCAGCAAATTCACCTGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:141769/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:1069712/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:3302555/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:3411451/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:2880294/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:355722/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:2593774/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:386948/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:2275023/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:1692752/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:1631197/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:643829/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:64669/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:800986/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:1121760/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:1188374/1‑69 (MQ=255)

acaGATAGGTTCAGCAAATTCACCCGCTTTCACCTCACCCTGATCGAAAGCGATTTCAATTCGGCTGcc                                                             >  1:1192466/1‑69 (MQ=255)

    aTAGGTTCAGCAAATTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCg                                                         <  1:776189/69‑1 (MQ=255)

    aTAGGTTCAGCAAATTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCg                                                         <  1:2818720/69‑1 (MQ=255)

    aTAGGTTCAGCAAATTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCg                                                         <  1:2691007/69‑1 (MQ=255)

    aTAGGTTCAGCAAATTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCg                                                         <  1:2069227/69‑1 (MQ=255)

     tAGGTTCAGCAAATTCACCCGCTTTCACTTCCGCCTGGTCGAGGGCGATTTCATTTTGGCTACCATCg                                                         <  1:2476411/68‑1 (MQ=255)

          tCAGCAAATTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTAc                                                              >  1:1029775/1‑58 (MQ=255)

          tCAGCAAATTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTAc                                                              >  1:1622564/1‑58 (MQ=255)

               aaaTTCACCCGCTTTCACTTCCCCCTGGTCGATGGCGATTTCAATTTGGCTACCATCGACCGc                                                    <  1:1456758/63‑1 (MQ=255)

               aaaTTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCa                                                            >  1:406751/1‑55 (MQ=255)

               aaaTTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCg                                                         <  1:1095256/58‑1 (MQ=255)

               aaaTTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCGACCGc                                                    >  1:1524311/1‑63 (MQ=255)

               aaaTTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCGACCGc                                                    >  1:472628/1‑63 (MQ=255)

               aaaTTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCGACCGc                                                    >  1:1180990/1‑63 (MQ=255)

               aaaTTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCGACCGc                                                    <  1:1370725/63‑1 (MQ=255)

               aaaTTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCGACCGc                                                    <  1:864649/63‑1 (MQ=255)

               aaaTTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCGACCGc                                                    >  1:279252/1‑63 (MQ=255)

               aaaTTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCGACCGc                                                    <  1:1583177/63‑1 (MQ=255)

               aaaTTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCGACCGc                                                    <  1:1553547/63‑1 (MQ=255)

                               aCTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCGACCGCCACCAGGCATTTTTCGCGATa                               >  1:2828906/1‑68 (MQ=255)

                               aCTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCGACCGCCACCAGCCATTTTTcgc                                   >  1:985674/1‑64 (MQ=255)

                               aCTTCACCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCGACCGCCACCAGCCATTTTTCGCGa                                 >  1:363322/1‑66 (MQ=255)

                                     cccTGGTCGAGGGCGATTTCAATTTGGCTACCATCGACCGCCACCAGCCATTTTTCGCGATAAAAATc                         <  1:1547458/68‑1 (MQ=255)

                                          gTCGAGGGCGATTTCAATTTGGCTACCATCGACCGCCACCAGCCATTTTTCGCGATAAAAATCGGTGc                    >  1:2756139/1‑68 (MQ=255)

                                          gTCGAGGGCGATTTCAATTTGGCTACCATCGACCGCCACCAGCCATTTTTCGCGATAAAAATCGGTGc                    >  1:671826/1‑68 (MQ=255)

                                          gTCGAGGGCGATTTCAATTTGGCTACCATCGACCGCCACCAGCCATTTTTCGCGATAAAAATCGGTGc                    >  1:2452604/1‑68 (MQ=255)

                                          gTCGAGGGCGAGTTCAATTTGGCTACCATCGACCGCCACCAGCCATTTTTcgcg                                  >  1:2571096/1‑54 (MQ=255)

                                                ggCGATTTCAATTTGGCTACCATCGACCGCCACCAGCCATTTTTCGCGATAAAAATCGGTGCTGAACAg             >  1:1081808/1‑69 (MQ=255)

                                                        cAATTAGGCTGCCATCGACCTCTACTAGCCATTTTTCGCGATAAAAATc                         <  1:749035/49‑1 (MQ=255)

                                                        cAATTAGGCTGCCATCGACCTCTACTAGCCATTTTTCGCGATAAAAATc                         <  1:1439456/49‑1 (MQ=255)

                                                        cAATTAGGCTGCCATCGACCTCTACTAGCCATTTTTCGCGATAAAAATc                         <  1:1430719/49‑1 (MQ=255)

                                                         aaTTAGGCTGCCATCGACCTCTACTAGCCATTTTTCGCGATAAAAATc                         <  1:1540575/48‑1 (MQ=255)

                                                            ttGGCTACCATCGACCGCCACCAGCCATTTTTCGCGATAAAAATCGGTGCTGAACAGCGGCTGCAcgc  >  1:1866976/1‑68 (MQ=255)

                                                            ttGGCTACCATCGACCGCCACCAGCCATTTTTCGCGATAAAAATCGGTGCTGAACAGCGGCTGCAcgc  >  1:1557773/1‑68 (MQ=255)

                                                            ttGGCTACCATCGACCGCCACCAGCCATTTTTCGCGATAAAAATCGGTGCTGAACAGCGGCTGCAcgc  >  1:365556/1‑68 (MQ=255)

                                                            ttGGCTACCATCGACCGCCACCAGCCATTTTTCGCGATAAAAATCGGTGCTGAACAGCGGCTGCAcgc  >  1:2960959/1‑68 (MQ=255)

                                                            ttGGCTACCATCGACCGCCACCAGCCATTTTTCGCGATAAAAATCGGTGCTGAACAGCGGCTGCAcgc  >  1:707086/1‑68 (MQ=255)

                                                            ttGGCTACCATCGACCGCCACCAGCCATTTTTCGCGATAAAAATCGGTGCTGAACAGCGGCTGCAcgc  >  1:838012/1‑68 (MQ=255)

ACAGATAGGTTCAGCAAATTCACCCGCTTTCACTTCCCCCTGGTCGAGGGCGATTTCAATTTGGCTACCATCGACCGCCACCAGCCATTTTTCGCGATAAAAATCGGTGCTGAACAGCGGCTGCACGC  >  minE/2051208‑2051335

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