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 I2 R1	764	42.0	2018750	95.5%	1927906	109.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,548,854	C→T	S16L (TCG→TTG)	fimH →	minor component of type 1 fimbriae

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,548,854	0	C	T	100.0%	128.6 / NA	40	S16L (TCG→TTG)	fimH	minor component of type 1 fimbriae
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (22/18); total (22/18)

AGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCG  >  NC_000913/4548734‑4548987

aGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCAtt                                                                                                                     >  2:344927/1‑139 (MQ=255)

 gCCACTCAGGGAACCATACAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTc                                                                                                                    <  2:394325/139‑1 (MQ=255)

                aTTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGcc                                                                                                     <  2:130852/139‑1 (MQ=255)

                 ttCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAAcc                                                                                                        >  2:607023/1‑135 (MQ=255)

                 ttCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAACAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAAcc                                                                                                        <  1:607023/135‑1 (MQ=255)

                    aGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTa                                                                                                                                   <  2:921689/105‑1 (MQ=255)

                    aGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTa                                                                                                                                   >  1:921689/1‑105 (MQ=255)

                                    cACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTAt                                                                                 >  2:161338/1‑139 (MQ=255)

                                               aCAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCa                                                                      >  1:88726/1‑139 (MQ=255)

                                                cAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAg                                                                     >  2:88051/1‑139 (MQ=255)

                                                 aGCTGAACCCGCATAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCa                                                                                                                       <  1:721026/88‑1 (MQ=255)

                                                 aGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCa                                                                                                                       >  2:721026/1‑88 (MQ=255)

                                                 aGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAgc                                                                    >  2:743951/1‑139 (MQ=255)

                                                 aGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAgc                                                                    >  1:882720/1‑139 (MQ=255)

                                                    tGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGcc                                                                 <  2:174942/139‑1 (MQ=255)

                                                      aaCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCaa                                                               >  1:1000922/1‑139 (MQ=255)

                                                        cccGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATg                                                             >  1:541125/1‑139 (MQ=255)

                                                        cccGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATg                                                             <  2:541125/139‑1 (MQ=255)

                                                         ccGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGt                                                            <  1:88051/139‑1 (MQ=255)

                                                         ccGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGt                                                            <  1:778116/139‑1 (MQ=255)

                                                                   gatTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGt                                                            >  1:948931/1‑129 (MQ=255)

                                                                   gatTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGt                                                            <  2:948931/129‑1 (MQ=255)

                                                                           tGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGcc                                          <  2:503628/139‑1 (MQ=255)

                                                                                cGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAAcc                                                                                                        <  1:429053/72‑1 (MQ=255)

                                                                                cGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAAcc                                                                                                        >  2:429053/1‑72 (MQ=255)

                                                                                             tGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGcc                                                                 <  1:237901/98‑1 (MQ=255)

                                                                                             tGTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGcc                                                                 >  2:237901/1‑98 (MQ=255)

                                                                                              gTTTGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCaa                       >  2:457246/1‑139 (MQ=255)

                                                                                               tttGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCTCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCcgtcgt                                    <  1:575033/125‑1 (MQ=255)

                                                                                               tttGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCt                                                                                         <  2:694785/72‑1 (MQ=255)

                                                                                               tttGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCt                                                                                         >  1:694785/1‑72 (MQ=255)

                                                                                               tttGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCcgtcgt                                    >  2:575033/1‑125 (MQ=255)

                                                                                                 tGCTGTACTGCTGATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAAc                    >  2:588581/1‑139 (MQ=255)

                                                                                                           ctgATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGccc                                         >  2:620432/1‑108 (MQ=255)

                                                                                                           ctgATGGGCTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGccc                                         <  1:620432/108‑1 (MQ=255)

                                                                                                                   cTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTa                                                                                  <  2:461038/59‑1 (MQ=255)

                                                                                                                   cTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTa                                                                                  >  1:461038/1‑59 (MQ=255)

                                                                                                                   cTGGTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTGATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCg  >  2:98552/1‑139 (MQ=255)

                                                                                                                     ggTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATgg                                                                                                <  2:371862/43‑1 (MQ=255)

                                                                                                                     ggTTGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATgg                                                                                                >  1:371862/1‑43 (MQ=255)

AGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCG  >  NC_000913/4548734‑4548987

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A