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	2,246,725	T→C	49.2%	R146R (CGT→CGC)	thiC →	thiamin (pyrimidine moiety) biosynthesis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,246,725	0	T	C	49.2%	‑6.0 / 53.2	59	R146R (CGT→CGC)	thiC	thiamin (pyrimidine moiety) biosynthesis protein
Reads supporting (aligned to +/- strand): ref base T (21/9); new base C (12/17); total (33/26)
Fisher's exact test for biased strand distribution p-value = 3.70e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.77e-01

GACGAACTGCGTTTTAGCGGCGTACTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACGCCGGAAATGGAATTCATC  >  minE/2246669‑2246782

gacgaGCTGCGTTTTAGCGGCGTATTAACGCCAAAACGCGCCAAAGCAGGACGCCGCGTCACCCAACTg                                               >  1:944511/1‑69 (MQ=255)

gacgaGCTGCGTTTTAGCGGCGTATTAACGCCAAAACGCGCCAAAGCAGGACGCCGCGTCACCCAACTg                                               >  1:1109696/1‑69 (MQ=255)

gacgaGCTGCGTTTTAGCGGCGTATTAACGCCAAAACGCGCCAAAGCAGGACGCCGCGTCACCCAACTg                                               >  1:675205/1‑69 (MQ=255)

gacgaGCTGCGTTTTAGCGGCGTATTAACGCCAAAACGCGCCAAAGCAGGACGCCGCGTCACCCAACTg                                               >  1:472573/1‑69 (MQ=255)

gacgaGCTGCGTTTTAGCGGCGTATTAACGCCAAAACGCGCCAAAGCAGGACGCCGCGTCACCCAACTg                                               >  1:1189836/1‑69 (MQ=255)

gacgaGCTGCGTTTTAGCGGCGTATTAACGCCAAAACGCGCCAAAGCAGGACGCCGCGTCACCCAACTg                                               >  1:390441/1‑69 (MQ=255)

gacgaGCTGCGTTTTAGCGGCGTATTAACGCCAAAACGCGCCAAAGCAGGACGCCGCGTCACCCAACTg                                               >  1:3335778/1‑69 (MQ=255)

gacgaGCTGCGTTTTAGCGGCGTATTAACGCCAAAACGCGCCAAAGCAGGACGCCGCGTCACCCAACTg                                               >  1:1355089/1‑69 (MQ=255)

gacgaGCTGCGTTTTAGCGGCGTATTAACGCCAAAACGCGCCAAAGCAGGACGCCGCGTCACCCAACTg                                               >  1:2542124/1‑69 (MQ=255)

gacgaGCTGCGTTTTAGCGGCGTATTAACGCCAAAACGCGCCAAAGCAGGACGCCGCGTCACCCAACTg                                               >  1:1043476/1‑69 (MQ=255)

gacgaGCTGCGTTTTAGCGGCGTATTAACGCCAAAACGCGCCAAAGCAGGACGCCGCGTCACCCAACTg                                               >  1:1941002/1‑69 (MQ=255)

gacgaGCTGCGTTTTAGCGGCGTATTAACGCCAAAACGCGCCAAAGCAGGACGCCGCGTCACCCAACTg                                               >  1:1834944/1‑69 (MQ=255)

gacgaACTGCGTTTTAGCGGCGTACTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTg                                               >  1:2146413/1‑69 (MQ=255)

gacgaACTGCGTTTTAGCGGCGTACTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTg                                               >  1:3198268/1‑69 (MQ=255)

gacgaACTGCGTTTTAGCGGCGTACTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTg                                               >  1:2081091/1‑69 (MQ=255)

      cTGCGTTTTAGCGGCGTACTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTAc                                         >  1:1182913/1‑69 (MQ=255)

      cTGCGTTTTAGCGGCGTACTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTAc                                         >  1:121789/1‑69 (MQ=255)

      cTGCGTTTTAGCGGCGTACTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTAc                                         >  1:3415925/1‑69 (MQ=255)

      cTGCGTTTTAGCGGCGTACTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTAc                                         >  1:2837250/1‑69 (MQ=255)

      cTGCGTTTTAGCGGCGTACTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTAc                                         >  1:1605792/1‑69 (MQ=255)

      cTGCGTTTTAGCGGCGTACTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTAc                                         >  1:1468344/1‑69 (MQ=255)

           ttttAGCGGCGTACTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTAcgcc                                      <  1:334542/67‑1 (MQ=255)

           ttttAGCGGCGTACTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTAcgcc                                      <  1:2655006/67‑1 (MQ=255)

                       aCTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGcatcat                        <  1:1629280/69‑1 (MQ=255)

                       aCTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGcatcat                        <  1:2091667/69‑1 (MQ=255)

                       aCTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCAACCAACTGCACTACGCCCGCCAGGGcatcat                        <  1:141995/69‑1 (MQ=255)

                        cTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCatcatc                       >  1:2104782/1‑69 (MQ=255)

                           acacCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACg                    >  1:2104067/1‑69 (MQ=255)

                           acacCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACg                    >  1:465861/1‑69 (MQ=255)

                           acacCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACg                    >  1:1551323/1‑69 (MQ=255)

                                aaaaCGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACGCCGGa               <  1:1427570/69‑1 (MQ=255)

                                aaaaCGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACGCCGGa               <  1:1751542/69‑1 (MQ=255)

                                aaaaCGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACGCCGGa               <  1:1780113/69‑1 (MQ=255)

                                 aaaCGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACGCCGGa               <  1:2755234/68‑1 (MQ=255)

                                          aaaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:284996/69‑1 (MQ=255)

                                          aaaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:3306094/69‑1 (MQ=255)

                                          aaaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:3302419/69‑1 (MQ=255)

                                          aaaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:1366995/69‑1 (MQ=255)

                                          aaaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:3154560/69‑1 (MQ=255)

                                          aaaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:1565084/69‑1 (MQ=255)

                                          aaaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:2578764/69‑1 (MQ=255)

                                          aaaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:2514869/69‑1 (MQ=255)

                                          aaaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:924812/69‑1 (MQ=255)

                                          aaaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:227194/69‑1 (MQ=255)

                                           aaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:2015781/68‑1 (MQ=255)

                                           aaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:830291/68‑1 (MQ=255)

                                           aaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:1349578/68‑1 (MQ=255)

                                           aaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:1813429/68‑1 (MQ=255)

                                           aaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:2010695/68‑1 (MQ=255)

                                           aaGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:1749203/68‑1 (MQ=255)

                                            aGCAGGACGCCGCGTCACCCAACTGCACTACGCCCGCCAGGGTATCATCACACCCGAAATGGAATTc     <  1:1175380/67‑1 (MQ=255)

                                              cAGGACGCGGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACGCCGGAAATGGAATTCATc  >  1:3417825/1‑68 (MQ=255)

                                              cAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACGCCGGAAATGGAATTCATc  >  1:1074289/1‑68 (MQ=255)

                                              cAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACGCCGGAAATGGAATTCATc  >  1:792896/1‑68 (MQ=255)

                                              cAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACGCCGGAAATGGAATTCATc  >  1:719279/1‑68 (MQ=255)

                                              cAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACGCCGGAAATGGAATTCATc  >  1:65244/1‑68 (MQ=255)

                                              cAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACGCCGGAAATGGAATTCATc  >  1:2688423/1‑68 (MQ=255)

                                              cAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACGCCGGAAATGGAATTCATc  >  1:2385964/1‑68 (MQ=255)

                                              cAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACGCCGGAAATGGAATTCATc  >  1:2211376/1‑68 (MQ=255)

GACGAACTGCGTTTTAGCGGCGTACTAACACCAAAACGCGCCAAAGCAGGACGCCGTGTCACCCAACTGCACTACGCCCGCCAGGGCATCATCACGCCGGAAATGGAATTCATC  >  minE/2246669‑2246782

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