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 2,036,477 T→C 41.3% T203T (ACT→ACC)  ygiC → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,036,4770TC41.3% 31.9 / 67.3 92T203T (ACT→ACC) ygiChypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (5/49);  new base C (22/16);  total (27/65)
Fisher's exact test for biased strand distribution p-value = 5.59e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCGGGTTAGGTGAAAA  >  minE/2036423‑2036515
                                                      |                                      
tCGCGGAACCATTCAGTATTTTCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGt                                    >  1:3356016/1‑59 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTAc                            >  1:2685953/1‑67 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:1022197/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:2144031/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:2131061/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:415585/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:2329393/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:2424617/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:2005623/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:658036/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:190769/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:2718984/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:2792417/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:282495/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:1062685/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:301915/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:925888/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:852893/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:2893847/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:1556492/1‑68 (MQ=255)
tCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:3185465/1‑68 (MQ=255)
tCGCGGAACCATTAAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATCGCTACCGAGTTCCTCTACa                           >  1:2019962/1‑68 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTTAAATTGCTACTGAGTTCCTCTACATCg                        <  1:1529786/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:3335341/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:2972645/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:2832573/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:3016324/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:3050430/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:2268678/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:2213741/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:3038624/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:672878/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:1606436/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:1633886/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:1659035/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:2044815/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:1093432/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:2076411/69‑1 (MQ=255)
  gcgGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:351848/69‑1 (MQ=255)
  gcagAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCg                        <  1:3420950/66‑1 (MQ=255)
    ggAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCgat                      <  1:2290628/69‑1 (MQ=255)
    ggAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCgat                      <  1:3091003/69‑1 (MQ=255)
    ggAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCgat                      <  1:1734481/69‑1 (MQ=255)
    ggAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCgat                      <  1:1536444/69‑1 (MQ=255)
    ggAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCgat                      <  1:3310052/69‑1 (MQ=255)
    ggAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCgat                      <  1:79056/69‑1 (MQ=255)
    ggAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCgat                      <  1:1065673/69‑1 (MQ=255)
          aTTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATc                <  1:1415372/69‑1 (MQ=255)
          aTTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATc                <  1:2096735/69‑1 (MQ=255)
            tCAGTTTTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:959009/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:816666/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:3325002/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:316250/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:770255/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:826034/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:3413827/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:433943/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:347117/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:2791057/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:3039850/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:1054349/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:280680/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:1649324/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:1782722/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:1901502/69‑1 (MQ=255)
            tCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTCCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:2887573/69‑1 (MQ=255)
             cAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              >  1:682187/1‑68 (MQ=255)
                  tttGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCgat                      >  1:457685/1‑55 (MQ=255)
                    tGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCGGGTTAgg        >  1:2881199/1‑67 (MQ=255)
                    tGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCGGGTTAgg        >  1:1337629/1‑67 (MQ=255)
                    tGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCGGGTTAGGt       >  1:2733605/1‑68 (MQ=255)
                        ggACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCGGGTTAGGTGaaaa  <  1:1577372/69‑1 (MQ=255)
                        ggACTGCGCAACGGAAGCTGAAATTGCTACTGACTTCCTCTACATCGATGATATCGGGTTAGGTGaaaa  <  1:2072818/69‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTat         <  1:375185/52‑2 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:2588552/52‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:1197088/52‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:1470767/52‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:799926/52‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:3294844/52‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:695014/52‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:506638/52‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:475340/52‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:2047522/52‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:2186501/52‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:2253314/52‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:2274175/52‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:237013/52‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:2541532/52‑1 (MQ=255)
                                  aCGGAAGCTGAAATCGCTACCGAGTTCCTCTACATCGACGATATCGGGTTAg         <  1:2699877/52‑1 (MQ=255)
                                   cGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:1980001/46‑1 (MQ=255)
                                   cGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:791378/46‑1 (MQ=255)
                                         cTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCgg              <  1:3263245/40‑1 (MQ=255)
                                                      |                                      
TCGCGGAACCATTCAGTATTTGCAGGACTGCGCAACGGAAGCTGAAATTGCTACTGAGTTCCTCTACATCGATGATATCGGGTTAGGTGAAAA  >  minE/2036423‑2036515

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