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
A6 F28 I1 R1	116	49.4	1663006	99.2%	1649701	139.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,462,889	(C)_9→10	intergenic (+243/‑123)	fadL → / → yfdF	long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,462,880	1	.	C	87.2%	116.9 / 10.7	39	intergenic (+234/‑132)	fadL/yfdF	long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF
Reads supporting (aligned to +/- strand): ref base . (2/3); new base C (14/20); total (16/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

TTGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATCATGCTACC  >  NC_000913/2462743‑2463019

ttGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑cc                                                                                                                                           >  2:151353/1‑140 (MQ=255)

 tGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑ccc                                                                                                                                          >  2:811917/1‑140 (MQ=255)

  gCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑cccc                                                                                                                                         <  2:810618/140‑1 (MQ=255)

  gCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑cccc                                                                                                                                         <  1:315753/140‑1 (MQ=255)

  gCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑cccc                                                                                                                                         <  1:416467/140‑1 (MQ=255)

  gCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAAGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑cccc                                                                                                                                         <  2:659281/140‑1 (MQ=255)

      aCAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑cccccccc                                                                                                                                     >  2:620865/1‑140 (MQ=255)

      aCAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑cccccccc                                                                                                                                     <  1:61605/140‑1 (MQ=255)

        aGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑cccccccccc                                                                                                                                   >  1:336750/1‑139 (MQ=255)

              ttGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCtt                                                                                                                              >  2:420717/1‑139 (MQ=255)

                     cTTGCCCTTTCAAATCAATAAGCGGTTTCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTTCTTTTCTGCATTTCCAGGATTCTC‑CCCCCCCCCTGGCTATTGTgcg                                                                                                                       <  1:420717/140‑1 (MQ=255)

                                aaaTCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTc                                                                                                            <  1:153338/140‑1 (MQ=255)

                                aaaTCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTc                                                                                                            <  1:804934/140‑1 (MQ=255)

                                       tAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTaa                                                                                                     >  1:559530/1‑140 (MQ=255)

                                          gCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGa                                                                                                  <  2:643230/140‑1 (MQ=255)

                                          gCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCA‑TTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGAt                                                                                                 <  2:170442/140‑1 (MQ=255)

                                              tATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAgg                                                                                              <  1:151353/140‑1 (MQ=255)

                                              tATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAgg                                                                                              >  1:77156/1‑140 (MQ=255)

                                                tCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGtt                                                                                            >  2:467462/1‑140 (MQ=255)

                                                tCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGtt                                                                                            <  2:262585/140‑1 (MQ=255)

                                                     aGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCtaaa                                                                                       >  1:124761/1‑140 (MQ=255)

                                                       aCAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGAt                                                                                                 <  2:377064/128‑1 (MQ=255)

                                                       aCAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGAt                                                                                                 >  1:377064/1‑128 (MQ=255)

                                                          aaCCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATg                                                                                 >  1:613882/1‑140 (MQ=255)

                                                            ccTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGa                                                                                >  1:323168/1‑140 (MQ=255)

                                                             cTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAg                                                                               <  1:467462/140‑1 (MQ=255)

                                                             cTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAg                                                                               <  1:10218/140‑1 (MQ=255)

                                                             cTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAg                                                                               <  2:336750/140‑1 (MQ=255)

                                                               gAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGt                                                                            >  1:647897/1‑140 (MQ=255)

                                                                     aaaGGCTTATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTTCTTTTCTGCATTTCCAGGATACT‑‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTg                                                                      <  1:811917/140‑1 (MQ=255)

                                                                     aaaGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGtttttt                                                                       >  1:796794/1‑140 (MQ=255)

                                                                     aaaGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGtttttt                                                                       >  1:277886/1‑140 (MQ=255)

                                                                      aaGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTg                                                                      <  2:323168/140‑1 (MQ=255)

                                                                       aGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGa                                                                     <  2:124761/140‑1 (MQ=255)

                                                                         gCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATa                                                                   <  1:464755/140‑1 (MQ=255)

                                                                                    ggCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCAtt                                                       <  1:620865/140‑1 (MQ=255)

                                                                                     gCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCAtt                                                       <  2:796794/140‑1 (MQ=255)

                                                                                        ttCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAg                                                                  >  1:680122/1‑126 (MQ=255)

                                                                                        ttCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAg                                                                  <  2:680122/126‑1 (MQ=255)

                                                                                        ttCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAgg                                                    <  1:73484/140‑1 (MQ=255)

                                                                                          cTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTa                                                  <  2:277886/140‑1 (MQ=255)

                                                                                          cTGCTCGTCCTTCTCAAAGAGTTTAATTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACCCTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTa                                                  <  2:199705/140‑1 (MQ=255)

                                                                                              tCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAatat                                              <  2:559530/140‑1 (MQ=255)

                                                                                                      ctcAAAGAGTTTGCTTTTCTGCATTTCCAGGATACT‑‑ACCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCTTTCGGTAATATATATTTGTa                                     <  2:41295/140‑1 (MQ=255)

                                                                                                               tttACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAaatca                             >  2:232608/1‑140 (MQ=255)

                                                                                                                ttACTTTTCTGCATTTCCAGGATACTCCCCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATAAGCGTTTTTTGATAGTCTATTTCATTAGGAAATATAAATTTGTAAAAaataa                             >  2:82648/1‑138 (MQ=255)

                                                                                                                ttACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAaatcaa                            >  1:676388/1‑140 (MQ=255)

                                                                                                                     tttCTGCATTTCCAGGATACT‑‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCaaaa                      <  2:613882/140‑1 (MQ=255)

                                                                                                                         tGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATGTATTTGTAACAAATCAATCAAAATgg                   >  1:580463/1‑140 (MQ=255)

                                                                                                                                         t‑‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATCATGCTAcc  >  2:394278/1‑140 (MQ=255)

TTGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATCATGCTACC  >  NC_000913/2462743‑2463019

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A