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	1,661,747	A→T	24.6%	intergenic (‑123/‑229)	yfgF ← / → yfgG	predicted inner membrane protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,661,747	0	A	T	24.6%	128.8 / 39.2	81	intergenic (‑123/‑229)	yfgF/yfgG	predicted inner membrane protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (32/29); new base T (7/13); total (39/42)
Fisher's exact test for biased strand distribution p-value = 2.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCTGACTTCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATGAATTATTACGTTTATCATGTTAATTCATC  >  minE/1661681‑1661815

aCCTGACTTCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTAcc                                                                    <  1:1771667/69‑1 (MQ=255)

aCCTGACTTCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTAcc                                                                    <  1:2215753/69‑1 (MQ=255)

aCCTGACTTCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTAcc                                                                    <  1:1890400/69‑1 (MQ=255)

aCCTGACTTCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTAcc                                                                    <  1:3023138/69‑1 (MQ=255)

aCCTGACTTCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTAcc                                                                    <  1:1587108/69‑1 (MQ=255)

aCCTGACTTCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTAcc                                                                    <  1:152155/69‑1 (MQ=255)

aCCTGACTTCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTAcc                                                                    <  1:1165408/69‑1 (MQ=255)

aCCTGACTTCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTATCATATGAAAGTAcc                                                                    <  1:788074/69‑1 (MQ=255)

       ttCGAATGATGATTATTCATCACTATAGAGAGTATTGATTCTAAGTGTCATATGAAAGTACCAATTg                                                               <  1:3046442/67‑1 (MQ=255)

       ttCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTg                                                               <  1:2387389/67‑1 (MQ=255)

       ttCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTg                                                               <  1:2391458/67‑1 (MQ=255)

       ttCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTg                                                               <  1:622957/67‑1 (MQ=255)

       ttCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTg                                                               <  1:2959044/67‑1 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            <  1:770323/69‑1 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            <  1:2704925/69‑1 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            >  1:2821524/1‑69 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            >  1:2827740/1‑69 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            <  1:2914231/69‑1 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            <  1:2955270/69‑1 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            <  1:3001283/69‑1 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            <  1:606454/69‑1 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            <  1:3303142/69‑1 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            >  1:1052008/1‑69 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            >  1:3313588/1‑69 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            >  1:3323430/1‑69 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            >  1:734586/1‑69 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            >  1:3355631/1‑69 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            <  1:356962/69‑1 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            >  1:371513/1‑69 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            <  1:459407/69‑1 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            >  1:1582118/1‑69 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            >  1:1662031/1‑69 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            >  1:1832056/1‑69 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            >  1:1855118/1‑69 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            <  1:1881317/69‑1 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            >  1:201391/1‑69 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGata                                                            >  1:2062487/1‑69 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGat                                                             >  1:2638597/1‑68 (MQ=255)

        tCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGat                                                             >  1:2081315/1‑68 (MQ=255)

         cGAATGATGATTATTCATCACTATAGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGata                                                            >  1:2303810/1‑68 (MQ=255)

         cGAATGATGATTATTCATCACTATAGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGata                                                            >  1:492052/1‑68 (MQ=255)

         cGAATGATGATTATTCATCACTATAGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGata                                                            >  1:3253692/1‑68 (MQ=255)

         cGAATGATGATTATTCATCACTATAGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGata                                                            >  1:3056759/1‑68 (MQ=255)

         cGAATGATGATTATTCATCACTATAGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGata                                                            >  1:2784869/1‑68 (MQ=255)

         cGAATGATGATTATTCATCACTATAGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGata                                                            >  1:2580227/1‑68 (MQ=255)

         cGAATGATGATTATTCATCACTATAGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGata                                                            >  1:2389644/1‑68 (MQ=255)

                           caCTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAAcc                                         <  1:147193/69‑1 (MQ=255)

                            aCTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTAcc                                                                    >  1:1343539/1‑41 (MQ=255)

                            aCTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTAcc                                                                    >  1:1953407/1‑41 (MQ=255)

                            aCTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTAcc                                                                    >  1:1819856/1‑41 (MQ=255)

                              tataGAGAGCATTGATTCTAAGTGTCATATGAAAGTAcc                                                                    <  1:815661/39‑1 (MQ=255)

                                taGAGAGCAATGATTCTAAGTGTCATATGACAGTTCCAATTGATATATATcaaacaa                                                <  1:2112424/57‑1 (MQ=255)

                                taGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGATATATATcaaacaa                                                <  1:2199598/57‑1 (MQ=255)

                                taGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGATATATATcaaacaa                                                <  1:2238047/57‑1 (MQ=255)

                                taGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGATATATATcaaacaa                                                <  1:1490972/57‑1 (MQ=255)

                                taGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGATATATATcaaacaa                                                <  1:2376396/57‑1 (MQ=255)

                                taGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGATATATATcaaacaa                                                <  1:2812153/57‑1 (MQ=255)

                                taGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGATATATATcaaacaa                                                <  1:2413524/57‑1 (MQ=255)

                                taGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGATATATATcaaacaa                                                <  1:2081013/57‑1 (MQ=255)

                                taGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGATATATATcaaacaa                                                <  1:2828731/57‑1 (MQ=255)

                                taGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGATATATATcaaacaa                                                <  1:268544/57‑1 (MQ=255)

                                taGAGAGCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGATATATATcaaacaa                                                <  1:3043937/57‑1 (MQ=255)

                                  gagagCATTGATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTa                                  >  1:3036375/1‑69 (MQ=255)

                                   agagCAATGATTCTAAGTGTCATATGAAAGTTCCAATTGATATATATcaaacaa                                                <  1:312193/54‑1 (MQ=255)

                                     agCATTGATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATg                               <  1:1795010/69‑1 (MQ=255)

                                     agCATTGATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATg                               <  1:664682/69‑1 (MQ=255)

                                     agCATTGATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATg                               <  1:365511/69‑1 (MQ=255)

                                     agCATTGATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATg                               <  1:1499720/69‑1 (MQ=255)

                                       cATTGATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATGa                              >  1:3071271/1‑68 (MQ=255)

                                       cATTGATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATGa                              >  1:1485435/1‑68 (MQ=255)

                                       cATTGATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATGa                              >  1:2889390/1‑68 (MQ=255)

                                       cATTGATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATGa                              >  1:748284/1‑68 (MQ=255)

                                       cATTGATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATGa                              >  1:319754/1‑68 (MQ=255)

                                           gATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATGAattat                         >  1:575497/1‑69 (MQ=255)

                                           gATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATGAattat                         >  1:312823/1‑69 (MQ=255)

                                                  aGTGTCATATGAAAGTTCCAATTGATATATATcaaacaa                                                <  1:40364/39‑1 (MQ=255)

                                                      tCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATGAATTATTACGTTTATCa              >  1:3129152/1‑69 (MQ=255)

                                                      tCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATGAATTATTACGTTTATCa              >  1:1299118/1‑69 (MQ=255)

                                                           tGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATGAATTATTACGTTTATCATGTTa         >  1:138829/1‑69 (MQ=255)

                                                           tGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATGAATTATTACGTTTATCATGTTa         >  1:1761679/1‑69 (MQ=255)

                                                           tGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATGAATTATTACGTTTATCATGTTa         >  1:1033163/1‑69 (MQ=255)

                                                                  aCCAATTGATATATATCAAACAAAATAACCCTGATTAATGAATTATTACGTTTATCATGTTAATtcatc  >  1:2321733/1‑69 (MQ=255)

ACCTGACTTCGAATGATGATTATTCATCACTATAGAGAGCATTGATTCTAAGTGTCATATGAAAGTACCAATTGATATATATCAAACAAAATAACCCTGATTAATGAATTATTACGTTTATCATGTTAATTCATC  >  minE/1661681‑1661815

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

GATK/CNVnator alignment

N/A