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	2,323,249	G→A	57.4%	intergenic (‑178/+142)	sbp ← / ← pfkA	sulfate transporter subunit/6‑phosphofructokinase I

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,323,249	0	G	A	57.4%	‑1.4 / 44.8	61	intergenic (‑178/+142)	sbp/pfkA	sulfate transporter subunit/6‑phosphofructokinase I
Reads supporting (aligned to +/- strand): ref base G (6/20); new base A (14/21); total (20/41)
Fisher's exact test for biased strand distribution p-value = 1.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

TAAAAAGGCGGAAGAAATCCGCCTCATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGCAGAATTCA  >  minE/2323183‑2323304

tAAAAAGGCGGAAGAAATCCGCCTCATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGcgcg                                                       <  1:2426987/69‑1 (MQ=255)

tAAAAAGGCGGAAGAAATCCGCCTCATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGcgcg                                                       <  1:3104344/69‑1 (MQ=255)

tAAAAAGGCGGAAGAAATCCGCCTCATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGcgcg                                                       <  1:2991581/69‑1 (MQ=255)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAg                               <  1:1169212/69‑1 (MQ=255)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAg                               <  1:459250/69‑1 (MQ=255)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:183798/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:2121511/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:1910081/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:2187319/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:1001586/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:2516951/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:653476/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:2794479/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:286925/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:512868/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:3116008/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:3184931/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:417455/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:374011/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:37678/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:397391/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:1273320/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:1073919/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:1408589/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCACAAAc                                                    <  1:1540068/48‑1 (MQ=17)

                        cATATTGCTGACAAAGTGCGCTTTGTACATGCCGGATGCGGCACAAAc                                                    <  1:1554476/48‑1 (MQ=14)

                             tGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTg                           >  1:1064894/1‑68 (MQ=255)

                                 gACAAAGTGCGCTTTGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTTCaaa                       <  1:2620483/68‑1 (MQ=255)

                                 gACAAAGTGCGCTTTGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCaaa                       <  1:1385809/68‑1 (MQ=255)

                                 gACAAAGTGCGCTTTGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCaaa                       <  1:2125670/68‑1 (MQ=255)

                                 gACAAAGTGCGCTTTGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCaaa                       <  1:1649136/68‑1 (MQ=255)

                                    aaaGTGCGCTTTGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:180414/1‑68 (MQ=255)

                                    aaaGTGCGCTTTGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:2871926/1‑68 (MQ=255)

                                    aaaGTGCGCTTTGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:1386749/1‑68 (MQ=255)

                                    aaaGTGCGCTTTGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:958873/1‑68 (MQ=255)

                                              ctGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGc          <  1:2728806/67‑1 (MQ=255)

                                              ctGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGc          <  1:3306489/67‑1 (MQ=255)

                                              ctGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGc          <  1:698479/67‑1 (MQ=255)

                                              ctGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGc          <  1:971674/67‑1 (MQ=255)

                                              ctGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGc          <  1:1590798/67‑1 (MQ=255)

                                                 tCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGCAg        <  1:1236845/67‑1 (MQ=255)

                                                 tCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGCAg        <  1:1251682/67‑1 (MQ=255)

                                                     tGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGCAGAATTCa  <  1:3271499/69‑1 (MQ=255)

                                                     tGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGCAGAATTCa  <  1:1406755/69‑1 (MQ=255)

                                                     tGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGCAGAATTCa  <  1:3097940/69‑1 (MQ=255)

                                                     tGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGCAGAATTCa  <  1:893766/69‑1 (MQ=255)

                                                     tGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGCAGAATTCa  <  1:2266794/69‑1 (MQ=255)

                                                     tGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGCAGAATTCa  <  1:1587931/69‑1 (MQ=255)

                                                     tGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGCAGAATTCa  <  1:211262/69‑1 (MQ=255)

                                                     tGCCGGATGCGGCACAAACGCCTTATCCGGCCTACAAAAGTTTGCAAAtt                     >  1:912549/1‑50 (MQ=14)

                                                     tGCCGGATGCGGCACAAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:2480956/1‑51 (MQ=14)

                                                     tGCCGGATGCGGCACAAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:731359/1‑51 (MQ=14)

                                                     tGCCGGATGCGGCACAAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:995193/1‑51 (MQ=14)

                                                     tGCCGGATGCGGCACAAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:335623/1‑51 (MQ=14)

                                                     tGCCGGATGCGGCACAAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:3272161/1‑51 (MQ=14)

                                                     tGCCGGATGCGGCACAAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:2974263/1‑51 (MQ=14)

                                                     tGCCGGATGCGGCACAAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:2711163/1‑51 (MQ=14)

                                                     tGCCGGATGCGGCACAAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:2173340/1‑51 (MQ=14)

                                                     tGCCGGATGCGGCACAAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:1595980/1‑51 (MQ=14)

                                                     tGCCGGATGCGGCACAAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:1448103/1‑51 (MQ=14)

                                                     tGCCGGATGCGGCACAAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:1247195/1‑51 (MQ=14)

                                                     tGCCGGATGCGGCACAAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:1173726/1‑51 (MQ=14)

                                                     tGCCGGATGCGGCACAAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTc                    >  1:1087660/1‑51 (MQ=14)

                                                       ccGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGCAGAATTCa  >  1:1011510/1‑67 (MQ=255)

TAAAAAGGCGGAAGAAATCCGCCTCATATTGCTGACAAAGTGCGCTTTGTCCATGCCGGATGCGGCGCGAACGCCTTATCCGGCCTACAAAAGTTTGCAAATTCAATAAATTGCAGAATTCA  >  minE/2323183‑2323304

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A