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	2,700,779	G→C	29.0%	A129A (GCG→GCC)	hofQ →	predicted fimbrial transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,700,779	0	G	C	29.0%	78.1 / 38.5	62	A129A (GCG→GCC)	hofQ	predicted fimbrial transporter
Reads supporting (aligned to +/- strand): ref base G (27/17); new base C (12/6); total (39/23)
Fisher's exact test for biased strand distribution p-value = 7.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.46e-01

GCAAATCTGCCGCTGGAAAATCGCAGTATAACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAGTATGACCGTCG  >  minE/2700729‑2700837

gCAAATCTGCCGCTGGAAAATCGCAGTATAACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCg                                          >  1:1282041/1‑69 (MQ=255)

gCAAATCTGCCGCTGGAAAATCGCAGTATAACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCg                                          >  1:1994876/1‑69 (MQ=255)

    aTCTGCCGCTGGAAAATCGCAATATTACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCgg                                         >  1:2099768/1‑66 (MQ=255)

    aTCTGCCGCTGGAAAATCGCAATATTACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCgg                                         >  1:264604/1‑66 (MQ=255)

    aTCTGCCGCTGGAAAATCGCAATATTACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCgg                                         >  1:2642503/1‑66 (MQ=255)

    aTCTGCCGCTGGAAAATCGCAATATTACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCgg                                         >  1:2738980/1‑66 (MQ=255)

    aTCTGCCGCTGGAAAATCGCAATATTACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCgg                                         >  1:2366843/1‑66 (MQ=255)

    aTCTGCCGCTGGAAAATCGCAATATTACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCgg                                         >  1:215338/1‑66 (MQ=255)

    aTCTGCCGCTGGAAAATCGCAATATTACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCgg                                         >  1:460513/1‑66 (MQ=255)

    aTCTGCCGCTGGAAAATCGCAATATTACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCgg                                         >  1:1943000/1‑66 (MQ=255)

    aTCTGCCGCTGGAAAATCGCAATATTACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCgg                                         >  1:1909212/1‑66 (MQ=255)

    aTCTGCCGCTGGAAAATCGCAATATTACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCgg                                         >  1:539940/1‑66 (MQ=255)

    aTCTGCCGCTGGAAAATCGCAATATTACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCgg                                         >  1:954930/1‑66 (MQ=255)

    aTCTGCCGCTGGAAAATCGCAATATTACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCgg                                         >  1:952115/1‑66 (MQ=255)

           gCTGGAAAATCGCAGTATAACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGc                                <  1:1749646/68‑1 (MQ=255)

           gCTGGAAAATCGCAGTATAACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGc                                <  1:1712715/68‑1 (MQ=255)

           gCTGGAAAATCGCAGTATAACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGc                                <  1:509261/68‑1 (MQ=255)

           gCTGGAAAATCGCAGTATAACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGc                                <  1:677295/68‑1 (MQ=255)

           gCTGGAAAATCGCAGTATAACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGc                                <  1:2297232/68‑1 (MQ=255)

           gCTGGAAAATCGCAGTATAACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGc                                <  1:611579/68‑1 (MQ=255)

              ggAAAATCGCAGTATAACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACt                            <  1:2148270/69‑1 (MQ=255)

                 aaaTCGCAGTATAACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTg                           <  1:2725159/67‑1 (MQ=255)

                 aaaTCGCAGTATAACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTg                           <  1:351391/67‑1 (MQ=255)

                          tattACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCGGGGGAGaa                                  <  1:229869/51‑1 (MQ=37)

                          tattACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCGGGGGAGaa                                  <  1:967038/51‑1 (MQ=37)

                          tattACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCGGGGGAGaa                                  <  1:1062280/51‑1 (MQ=37)

                          tattACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCGGGGGAGaa                                  <  1:3204842/51‑1 (MQ=37)

                          tattACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCGGGGGAGaa                                  <  1:825886/51‑1 (MQ=37)

                          tattACTCTGCAATACGCCGACGCCGGAGAGCTGGCGAAAGCGGGGGAGaa                                  <  1:616095/51‑1 (MQ=37)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGa                          >  1:2754609/1‑57 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:3305846/1‑68 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:870260/1‑68 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:2857918/1‑68 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:394649/1‑68 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:458485/1‑68 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:2565841/1‑68 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:2703990/1‑68 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:1822943/1‑68 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:2087989/1‑68 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:2286667/1‑68 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:2293210/1‑68 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:2440034/1‑68 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:1414822/1‑68 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:1112295/1‑68 (MQ=255)

                            taACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAggg               >  1:1064896/1‑68 (MQ=255)

                              aCCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAg             <  1:2500563/68‑1 (MQ=255)

                              aCCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAg             <  1:2469009/68‑1 (MQ=255)

                              aCCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAg             <  1:3354765/68‑1 (MQ=255)

                              aCCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAg             <  1:1164431/68‑1 (MQ=255)

                              aCCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAg             <  1:1123861/68‑1 (MQ=255)

                              aCCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAg             <  1:2517737/68‑1 (MQ=255)

                              aCCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAg             <  1:1998475/68‑1 (MQ=255)

                                        aCGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGc                                >  1:1868755/1‑39 (MQ=255)

                                        aCGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAATGGAGTATGACCGTc   >  1:3279882/1‑68 (MQ=255)

                                        aCGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAGTATGACCGTc   >  1:1063703/1‑68 (MQ=255)

                                        aCGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAGTATGACCGTc   >  1:1792395/1‑68 (MQ=255)

                                        aCGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAGTATGACCGTc   >  1:3030547/1‑68 (MQ=255)

                                        aCGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAGTATGACCGTc   >  1:2503988/1‑68 (MQ=255)

                                        aCGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAGTATGACCGTc   >  1:2760445/1‑68 (MQ=255)

                                        aCGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAGTATGACCGTc   >  1:2586189/1‑68 (MQ=255)

                                         cGCCGACGCGGGAGAACTGGCGAAAGCGGTGGAGAAGCTACTg                           <  1:3359088/43‑1 (MQ=255)

                                         cGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAGTATGACCGTCg  >  1:2606057/1‑68 (MQ=255)

GCAAATCTGCCGCTGGAAAATCGCAGTATAACCCTGCAATACGCCGACGCGGGAGAACTGGCGAAAGCGGGGGAGAAGCTACTGAGTGCCAAAGGGAGTATGACCGTCG  >  minE/2700729‑2700837

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A